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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. What to eat while taking antibiotics?
    Chicken and eggs are recommended while taking antibiotics?

  2. what about protecting your kidneys especially if you have reduced renal function?

  3. After a few weeks of sudden nausea, dizziness and not being able to eat, I had some bloodwork done and sure enough…..I tested positive to H Pylori. Initially, I had gone the natural route and took Pylori Plex….a natural supplement with mastic gum, licorice root, marshmallow root and slippery elm bark. Took once daily for three days and then decided to switch over to antibiotics……the natural route may have taken longer to eradicate the H Pylori and I didn’t want to go through my symptoms much longer. Also, the natural treatment works differently for everyone and so I thought to go direct for a week’s worth of very aggressive antibiotics to kill the bacteria. Totally against antibiotics but after weighing the pros and cons, I thought it best to take this route. I have been eating organic probiotic yogurt daily, even up to 3 times a day. Making my own applesauce just boiling apples and pear in some water and then mush everything to create a creamy thick juice. I also add some cinnamon. I am eating often throughout the day as my stomach alway feels empty and this creates nausea. The antibiotics also leave a strong medicine taste in my mouth ( it’s so difficult to sleep during the night time with these terrible symptoms.) So, my question is, what protein meals can I have other than chicken, that would satisfy my appetite and is longer lasting during the night time, considering my gut is going through traumatic stress? What about snacks? I also drink organic grass fed, free from GMO chicken bone broth which I make myself….I let the chicken bones simmer for 15 hours to get maximum nutrient and probiotic benefits adding turmeric, garlic, onion, carrots, tomato, and potato. Has anyone had H Pylori?

    • I had H Pylori and was prescribed triple therapy antibiotics for it without Nexium. They failed and I had holes in my gut. I started with autoimmune diseases immediately. I manage this with the AIP Paleo diet which works perfectly fine and changed all skin and body care using the Think Dirty App. Being endocrine related, I was reacting to my products.

      I took mastic gum (single supplement not mixed) 3 times a day with an auyervedic gut supplement (yellow box -as they’re colour coordinated). This cleared the h Pylori within 5 days.

      I recommend you buy Sarah Ballantyn’s book ‘guide to healing autoimmune disease’ as she explains the best way to heal and what foods can cross react or cause issue(s).

      Good luck!

  4. If someone has high strep titers, do probiotics with streptomyces strains (found in Prescript-Assist) need to be avoided?

  5. Very useful article, as is typically the case with Chris. In my experience in this type of situation, the best course of action has been to adopt a simplified paleo diet prior, during and after antibiotic use, with the daily inclusion of light amounts of leeks, asparagus and onions, as well as sweet potatoes, yams and plantains. Go easy on these prebiotic foods at first (especially if you’re eating Jerusalem Artichoke), or you’ll wind up with undesirable side effects.

    Eating fermented foods, and consuming a good broad-spectrum probiotic (Klaire Labs Therbiotic Complete or VSL #3 can be good choices), along with Prescript-Assist and Saccharomyces Boulardii (Klaire Labs or Designs for Health are both good), can create enough transient “good guys” to prevent the overgrowth of “bad guys”, which is ultimately the goal.

    Aside from that, dodging excessive exercise, drinking enough clean water, breathing enough clean air, creating simple movement and getting good sleep are also all important.

    Hope this helps!

  6. When having to take antibiotics, why not have injection. If there’s a barrier between blood and gut flora, flora would not be changed.

    • I was wondering the same thing.
      I am currently having high doses of antibiotics Intravenously, but will have to take a course of oral antibiotics once I am discharged from hospital.
      I suppose for now your query about just having it through an injection is fine, however hospitals don’t have the beds to do that for everyone. So ultimately everyone needing to take antibiotics will at some point have to take them orally in which case the guy biome is affected

      • I’ve read about IV boutiques in the US, there are a lot in CA, where you can drop by to get an IV of anything you want and just sit in a chair watching TV while it drips.

      • Not necessarily so, I’ve had a PIC line for antibiotics at home. A nurse came to my home every three days to change the bandage, and I would receive three days worth of prefilled pressurized balloons of antibiotics, prefilled saline and blood thinning syringes so I could administer myself, from a specialized pharmacist. It was a pain, but way better than occupying a bed in the hospital for two weeks.

  7. What do you suggest as a vegetarian source of glycine? (Bone broth being non veg.)


  8. I have to take 3 types of antibiotics for 2 weeks. I hate antibiotics but I need to kill parasites. What can you recommend to avoid skin rashes on the face while on antibiotics? Thank you

    • Ask you doctor to change your antibiotics. Although not a true allergic reaction, you are obviously sensitive to those antibiotics and the rash can increase to look like a full blown sunburn. A rash indicates a reaction and can become serious. My grown daughter has a rare immune disease and cannot fight infection on her own without antibiotics. She is reactive to many and as soon as she gets a rash on her face or trunk her doctors change her antibiotic. Keep a record of the antibiotic name you are “allergic” to.

    • Ask you doctor to change your antibiotics. Although not a true allergic reaction, you are obviously sensitive to those antibiotics and the rash can increase to look like a full blown sunburn. A rash indicates a reaction and can become serious. My grown daughter has a rare immune disease and cannot fight infection on her own without antibiotics. She is reactive to many and as soon as she gets a rash on her face or trunk her doctors change her antibiotic. Also take a dose of Benadryl immediately to stop the histamine reaction. Keep a record of the antibiotic name you are “allergic” to.

  9. I have spent three years getting my SIBO and leaky gut under control with big changes in my diet, supplements and finally an elemental diet. Last week I was prescribed antibiotics for strep throat. I was pretty ill and it was only three days later that I realised that although the throat and flu symptoms were improving my biome was in trouble. I had thrush, brain fog and fatigue worse than I had in a long time.

    BUT … this is a success story. I went back to my basic first aid diet of vegetables and bone broth with garlic, ginger and turmeric and upped the dose of my anti-candida supplement and probiotics. I can’t tolerate anything fermented so yoghurt and kefir etc are out, but I have a supplement with S boulardii. I take the supplements two hours before the antibiotics.

    So far I have only had diarrhea once and the candida symptoms are barely noticeable. And the brain fog etc is receding.

    I’m not thrilled about having my carefully nutured gut flora trampled over, but I think I made the right choice. I repaired my gut before, I can do it again if necessary. But if I got rheumatic fever, the damage could be permanent. If you have strep throat, don’t think twice! You need those antibiotics.

    Here is my recipe for starchy veg puree – I’ve been eating this for breakfast, lunch and dinner. It’s comfort food and the flavour improves with keeping.

    Chop 3 cloves garlic and a thumb sized piece of root ginger finely and saute in a big pot in 1 – 2 tbsp coconut or olive oil until fragrant but not brown. Add 2 tsp each turmeric and ground cumin, and tomato paste and chilli to taste, and cook stirring for a few mins. Add a whole heap (at least half your big pot full) of chopped up starchy veg. (I have used different combinations of carrot, pumpkin, rutabaga/swede, potato and beetroot.) Add water to barely cover the veg, put the lid on and simmer until completely soft, then whizz with a whizz stick, season with pepper etc, thin with almond milk if you want it more like soup, and eat. I often put finely chopped greens in too, but once it’s pureed it sticks to the bottom of the pot so can’t be cooked much longer without stirring.

    • Sounds like you are doing all the right things. I made my own Cleavers Tincture and use that when my neck glands tell me to. Prior to making the tincture I used raw cleavers from the garden to make tea and also had some dried to last through the winter. I recommend a probiotic that includes Streptococci strain also for prevention.

  10. I heard how good coconut oil was for you. I also found it caused a rise in my cholesterol. I stopped taking it everyday but still cook with it and use it for my essential oils, cleaning my face, and as a face/body oil

    • There are 2 kinds of cholesterol. One is bad and one is REALLY good for you. They usually test it as whole so they do not know which one got increaed. Coconut oil incraeses the good one. So please do not get scared and get more reasearch done before you stop using coconut oil. It is SO good for you!

  11. Over the summer of 2007, I developed an abscess pneumonia. Was functioning just fine the Friday prior. Helped a friend box things up and clean for her move. Next day my sides hurt while breathing. I have not forgotten that feeling from when I was 5/6 and had double staph pneumonia. Found out this had to have been festering for months. Likely from an unresolved sinus infection. It took me over in less than a day. Spent four days in hospital on IV levaquin and they said the bloodwork showed it to be something people walk in with and never walk out again. To clear the hole in my lung, I was on two months of oral levaquin combined with oral cipro. The first two weeks I was overdosed with the levaquin. A mistake found at my follow up appointment. Medical student wrote the script wrong. I was left with an empty hole in my lung so I had to have that lobe removed. Ever since this episode, I’ve had IBS symptoms, peripheral neuropathy, fibromyalgia, chronic fatigue syndrome……. None of of which affected me before this. I need to know what kind if regimen to get on to revitalize my gut. I’m certain it just hasn’t been the same since. What is safe to take with most medications and how long would I likely need to follow such a plan?
    Thank you

    • Jacq,

      I’m so sorry to hear about your ordeal that no one should ever have to go through. Did they tell you that your staph was MRSA?

      I was finally properly diagnosed with MRSA after having cellulitis from a shaving nick for the second time in a three month span. They put my on 10 days of oral antibiotics (Keflex and Bactrim) after having received an IV of antibiotics the first outbreak a few months back. Recently, I’ve been trying to follow my doctor’s orders on “decolonization” with bleach baths, which completely destroyed the good bacteria on my skin. I developed a severe UTI just a few days ago, my pulse was 137 and fever at 103.7. Worst pain throughout my body I ever felt in my life, but I knew I had to go to the ER and receive antibiotics (even though I refused). They put me on an IV with Rocephin and then 10 day course of Keflex. Of course I’m really concerned re my MRSA because it is resistant to beta-lactims, but I didn’t want Bactrim because that completely destroyed my gut flora.

      So what have I done? First for my MRSA, I purchased 100% stabilized allicin from Allimed, which is effective against killing MRSA and has saved the lives of so many. It’s expensive, but worth it. I take 4 teaspoons a day and will be for the next six months and a maintenance dose, forever. (I’m constantly around kids). I would call Optimal Health and ask if Allimed could help you out, as I know it helps people with Candida and Lyme. It was developed by a UK Infectious Disease Specialist and a Microbiologist, Dr. Ron Cutler.

      I’ve been on a special 50 billion probiotic blend I got from Whole Foods for women. Also, on Now’s D-Mannos I mix with juice (2000 mg) to help fight any infections in my kidney or UT, naturally.

      Allimed is definitely a must. It’s quite phenomenal. It is a very good immune system booster, which is how it enables the body to fight off infections.

      I wish you the best of luck. Keep us updated.

    • I would start on a powerful probiotic VSL3, available without a prescription but behind the pharmacy counter. It is expensive (apx $68 for 60 caps) and kept in the pharmacy refrigerator. My daughter has a rare immune disease and quite literally this probiotic has saved her life after many pneumonias and benign on prophlactic and IV treatment antibiotics for 13 years as well as a resection of her lower left lung lobe from a dangerous pneumonia and intestinal rupture with her transverse colon removed. VSL3 has been Worth every penny! She has been taking for 6 years now – 2-3 caps per day. But start slowly, one a day and build up.

  12. Chris recommends and sells Prescript Assist on his site. I read a very disturbing opinion at http://fixyourgut.com/hso-probiotics-part-3-prescript-assist/ which makes me question whether or not PS is all it’s cracked up to be. It would be great if we could get some clarification on these differing perspectives. The last thing many of us want is to take something that does harm to what are likely already delicate guts.

  13. I have been taking a monthly bicillin(antibiotic) shot once a month for rheumatic heart disease since I was 6, and I am now 34. Am I able to take probiotics? And will the probiotics benefit my gut and heart health?

  14. Just curious, if anyone is answering the questions in these comments, where does one go to find the answers?

  15. Chris & Team…

    As children often get sick, ear infections and the like, which sometimes do not resolve themselves. What would you recommend to protect and re-populate the gut of children, who are younger than the recommended ages on most probiotic supplements… talking 0-2yo. Yogurt, Kefir sour kraut etc i would guess, along with some cooled potatoes perhaps, But is there anything else?

    Thanks for all you do!


    • My child has had ear infections and a penis infection twice and I always use Innovative Natural Super Colloidal Silver 2000and he has never had to use antibiotics. I haven’t taken antibiotics since I was 12. We use FOS by allergy research Group and UP4 acidophilus for probiotics. Avoid sugar, dairy, yeast, wheat during the time of infection helps as well. There are alternatives out there. Even for infections like streptococcus and staphylococcus infections, both of which I’ve had and used herbs and silver to get over them.

  16. I really like all the good info on this site. Just one observation: in the 2nd paragraph after the heading Prebiotics, it says that potato starch is insoluble fiber. I just checked to reassure myself, but according to what I have read, insoluble fiber will not dissolve in water (that actually sounds like what ‘insoluble’ would mean). Also, they say that insoluble fiber generally passes through the gut intact. Soluble fiber does dissolve in water and is consumed by the flora in the gut. Potato starch definitely dissolves in water. So it doesn’t sound as if it could be called an insoluble fiber. At least one reference I checked put resistant starch in a class by itself. At any rate, not trying to nit pick.

    • The story states to eat soluble starch, such as the potato starch. It warns that insoluble starch can cause further issues because if it’s bulk and potential irritation it can cause. So insoluble is not recommended. Soluble potato starch is recommended 🙂