What To Do If You Need To Take Antibiotics | Chris Kresser
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What To Do If You Need To Take Antibiotics

by Chris Kresser

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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 such as this one.

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.

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!

I hope you found this article helpful. As always, I’d love to hear from you in the comment section; just be mindful that I’m busy with my book tour right now, and may not be able to reply to your questions. But many of my readers are extremely knowledgable, and I encourage you to take advantage of the free forum in addition to the comments section to bounce ideas and experiences around.


Join the conversation

  1. 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!

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

  3. 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!

  4. 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.

  5. 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.

  6. 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.

  7. 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!

  8. 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.

  9. 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.

  10. 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?

  11. 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.

  12. 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 🙂

  13. 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?

  14. 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.

  15. 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.

  16. 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.

  17. *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…

  18. 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.

  19. 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!

  20. 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.

  21. 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…

  22. 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)

  23. 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.

  24. 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)!!

  25. 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.

  26. 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?

  27. 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…

  28. 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.

  29. 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.?

  30. 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.

  31. 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

  32. I am 39.5 weeks pregnant. My 2.5 year old son was diagnosed with whooping cough 9 days ago and I was tested and got my results back 3 days ago. When I my son tested positive we both started a very strict diet recommended by my naturopath that is high in fruit and vegetables and we are excluding grains (still eating oats with chia and LSA) and no dairy, that included high vitamin c supplements and I was taking a mix of raw garlic, onion and manuca honey, and we have been on lots of bone broth.
    However when I got my results back and I was positive it was very firmly recommended to start s course of antibiotics (clarithromycin) to make sure we are not still contagious when the baby is born. We started them 3 days ago, I am taking probiotics, continuing with the diet my naturopath recommended and introduced coconut kefir, and dill sauerkraut which are both store bought. My mother in law is making me some homemade kefir.
    I really want to get my gut bacteria into the best condition before the baby is born, hoping the baby comes late to give me more time. Can you recommend anything else I can do?

  33. On the rare occasion I have had to take antibiotics, I can definitely feel my body is off. I have terrible cravings, no energy, and an overall sense of blah. After the antibiotic cycle is complete, I have found a healthy diet of nutrient dense foods, fermented foods and quality probiotics, I also take a liver blend of essential oils to support natural detoxification. I just found a new line of clinical grade essential oils and they have been a very beneficial addition to my family’s life! I got them at honest.oils.myameo.com if anyone is interested.

  34. Hi Chris

    I am 36 weeks pregnant and have just been diagnosed with GBS in urine. Have been prescribed amoxicillin.

    I had been on a strict regime to eradicate gbs and the vaginal swab came back negative.

    Is there anything else you think I could do instead of taking the antibiotic?

    Doctors are also saying I should take in labour.

    If I did have treatment, what can I do other than breastfeed, skin to skin and give probiotics to help newborns microbiome?


  35. I have also been diagnosed with MAC and bronchiectasis. It took 2ys to establish a diagnosis and there is a moderate damage to my lungs already. I am otherwise a 42-yo healthy non immunocompromised, non-smoking woman.
    Although I am terrified of the potential side effects of the three-antibiotics treatment for Mac, this includes blindness and deafness, I started this treatment three days ago. I already have mild side effects – extreme fatigue, somnolence, and excessive bowl movements without diarrhea and slight abdominal pain. All is mild and I can tolerate it so far and determined to continue.
    Unfortunately this treatment, in my case Myambutol (Ethambutol), Rifampin and Azithromycin, might go on for years if I don’t become blind or deaf during it. However, I have to get this infection treated and would like to manage the side effects better. A professional advice would be immensely helpful. My physician is great regarding MAC treatment but not with anything beyond the Western medicine. What could help to reduce the possible dreadful side effects?
    I purchased Jarrow Formulas Jarro-dophilus EPS and will start it tonight. Was thinking about taking milk thistle but was told that it might increase the potential side effects of the antibiotics. Sadly, I just cannot get any question about how to manage these side effects and still in the midst of the unknown.
    I would greatly appreciate an educated piece of advice or someone else’s successful MAC treatment story.
    Thank you!

    • Lydia, I am starting the treatment too and am very scared. Are you done now? How did it go? and I’m hoping you don’t say anything too bad because I really need to do this and am so scared.

  36. I am caring for my elderly mother who has advanced Akzheimers Disease and other ailments. At the moment I have her on cephalexin for a uti. She is unable to tolerate dairy or fermented foods. Can I still give her her probiotics? How long after the antibiotic?

    Thank you

  37. Do you have any information or resources on long term antibiotic use during pregnancy? I have chronic Lyme Disease and have treated it naturally for years. I’ve been advised (by a naturopath who does not readily prescribe them) to take antibiotics during pregnancy to reduce the risk of passing the bacteria to baby. My concern is that the antibiotics will negatively effect the baby’s microbiome and immune system. Any info, studies, etc you could direct me to?

    • That’s interesting that the naturopath thinks you should take antibiotics. I don’t have a clear answer for you.

      Antibiotics can be a double edged sword. They can help and hurt. What antibiotic does he say you should take and what did he say to your concerns ?

      Make sure your baby isn’t given any vaccines.

      They always say that pregnant women shouldn’t take this or that supplement without a doctors ok. Of course if your doctor is one of the few who knows about nutrition then it may be a different story.

      There are two products that are proven thru research to help the immune system, they are moducare and micronized beta glucans. Moducare balance overactive and underactive immune systems. The micronized beta glucan helps the Th1 and it is the only beta glucan that works. The regular high mg beta glucan does not work.

      I’d consider taking higher than normal doses of nutrition. In autism for instance, they say what causes the damage is that the selenium get depleted. I think if the baby has sufficient nutrition, it improves the odds.

      • Antibiotics are recommended during pregnancy because research has shown they greatly reduce the risk of passing the infection on to the baby. In the presence of antibiotics the spirochete goes into a form of “hiding”. They are recommending amoxicillin or azithromyocin. Their opinion is that the benefits out weigh the risks in this case, but I still feel uneasy about it.

        The herbal remedies I am currently taking haven’t been studied during pregnancy, so we don’t know how safe they are during pregnancy or effective they are at preventing transmission.

      • Please don’t pressure people not to immunise their babies.

        Everyone is entitled to make up their own minds but they should be aware of the science and history behind diseases such as measles, whooping cough and polio before making their decision.

        Babies and children still die today from whooping cough and measles: these diseases are still very much out there in the community.

  38. I have to take antibiotics for a ‘bacterial’ case of bronchitis – that I now realized was from acid reflux and eating some possible tainted meat. I was very sick so ultimately relented to antibiotic. Was prescribed Azirthromycin after just 2 doses I had diarrhea – so now was given Keflex.
    I started taking sacrro 2xa day – and I had Klair Labs probiotics (Factor 1 ) which helps with diarrhea. It has seemed to help calm everything down but my problem now is a loss of appetite. I have to start Keflex tomorrow – and so worried as to whether the antiobiotics are going to damage all the work that I have done on my digestive issues.
    I did take some notes on comments below – lglutamine and will get GSE oil. What are recommendations for loss of appetitie and what causes that ?

    • I have been on Augmentin 875 mg twice a day for 10days in Dec, 2014 for a sinus infection, then in Jan. 2015 got on 250mg Ciprofloxacin twice a day for five days, that was for a UTI , I go back to be checked in Feb., 2015 and it didn’t get rid of it so they put me on Bactrim twice a day 875 mg and then got the flu I call it the doc called it a virus, but I ached, had low grade fever with chills, cough and coughing up clear sputum but have never coughed up as much for as long and couldn’t eat or drink during this time but tried to sip on few fluids and crackers. Then I started with blood in my urine the third week of the flu actually blood in urine making it red due to I guess not drinking and urinating as often, so I go to urgent care in March 7, 2015 and they put me on 500 mg of Ciprofloxacin twice a day for seven days and I stopped on the 7th day completed that seven days on the 13th of March and today is March 15th. How do I get back to normal with my strength as I am 65-1/2, have been healthy other than a UTI about once a year since I turned 60 I think. I am weak and bought Probiotics but haven’t started taking yet due to being so afraid that it may start something else up, or I have had reactions to certain things in the far past. I am not sure what to do.

  39. I am a healthy 57 yr. old woman. I have been diagnosed with H Pylori bacteria. I was tested for this because of tightness in my chest and irregular heart beat.
    ( an EKG and test for blood clots was also given prior).
    I’m on, due to choice, mega doses of antibiotics and thus found your article as I was concerned about taking 8 large meds a day.
    The good news is my heartbeat and tightness are gone.
    But I am not sure how much milk thistle and probiotics to take. Garden of Eden has a probiotic grown in soil I will take and the S. BOulardi I have on board.
    Any suggestions on Milk Thistle or other items to consider?
    I have read your article above twice and made notes.
    Thank you! Great article and support. Susie

      • Thank you for the info on H Pylori. Very interesting to know there are solutions to deal with this bacteria without using antibiotics. I choose to use them since I was having
        serious irregular heart beat issues and wanted to be sure these were addressed.
        As we know this is also no guarantee. I am not 100% convinced now that this was the H Pylori was the cause. Rather I am now thinking it may have to do with hypothyroid and
        Hashimotos antibodies. I seem to have a trigger, chocolate. I talked to a pharmacist who recommended I try Glutathione and go off my compounded T3/T4 for 1 day.
        This converted my heart rate back to normal. I am taking care and following Chris’s suggestions while I finish the antibiotic protocol. Thank you again for the info.

        • Hello Susie… Can you email some of the things you took for your heart I have the same issues with my heart. And now I’m sick with ear pain and a sore throat the Dr. gave me Amoxicillon but I feel like its not helping me it’s hurting me.

  40. Hi Chris and friends,

    I haven’t taken antibiotics for years and then last month had a scorching UTI which I took 3 rounds of antibiotics for followed by fluconazole, AKA: drug from hell.

    I have had a stomach ache all week but yesterday it was stomach ache with delirium, joint ache, headache, exhaustion, and chills. I started researching and thought (think?) maybe its because of a toxic liver from all the meds. I have been resting now for 24 hours, doing coffee enemas, drinking dandelion tea, eating cooked vegetables, salt baths, etc. I’m doing all that I can – I am afraid that this is early sign of acute liver failure or drug induced hepatitis?

    I woke up feeling MUCH better but am still tired, not hungry, stomach ache. Should I go to the ER? Proceed as I am doing? Other ideas? I don’t feel like it’s an emergency right now, maybe I’m on the upswing?

    • FYI

      there are many remedies for UTI’s. No need to resort to antibiotics.

      For E. Coli, there is D-mannose or cranberry capsules.

      For other UTI infection, there is Uva Utis capsules which is very potent. You take two 450mg capsules with alkaline water (1 tsp of baking soda in water). The alkaline solution is important because the herb requires an alkaline solution to release active ingredient. Take it twice a day.

      • I have a problem taking antibonics the dr just gave me kelfex for uti i dont do well with any antibonics my stamach hurts and i jave lbs so it makes it worse my mouth dry and my muscles hurt i am allegic to sulfa And penillian i wish there was something i could take thats natural with no side effects can you help me thamk you

  41. I used to have a lot of respiratory infections, every year during winter season, last time I had bronchitis, and I had to take antibiotics every time. After my treatment, I went to this Dr. who gave me a diet called Food Combination and I had to take, first time in the morning, one lemon, a little piece of fresh peeled ginger, one tbsp of honey and 1 small glass of water, everything goes to the blender, washed the lemon and the ginger very well, and dont forget to peel the ginger, and the lemon goes with everything you just cut it in 4 and the ginger cut it in small pieces. you liquify this and use the colander and drink it with a straw, to protect your teeth. Some people experience a little softness in their bowels, I dont. Since then, I havent experience a cold or flu or anything like it. No flu or cold in 4 years, and I am 55. Hopes this helps.

  42. Hey chris i had a question, ive been on and off about 3 antibiotic prescriptions in the past month and ahalf from different infections. This most recent infection is strep throat. I feel it slowly going away without antibiotic treatment but im really worried about the complications of strep without antibiotic treatment. And advice will be greatly appreciated!

      • Yes strept can lead to heart problems scarlet fever, etc. Go see a doctor. It doesn’t just go away by itself. U may become immuned and then become what is called a “carrier”. Be safe rather than sorry!

  43. Does anyone know if there a natural way of combating respiratory infection with the same power and speed as an antibiotic? I eat fermented food, kefir water and kefir milk, but I have to go on antibiotics at the first hint of a respiratory infection due to asthma and reactive airway that was caused by intubation. I’m on antibiotics now, but they’re not helping my lungs much. I wanted to take probiotics, but was afraid it would negate the antibiotic.

  44. Hi Chris, my adult daughter has recently been diagnosed with Rhuematic fever. She is 27 and the mother of 4 boys. It came on very quickly, with in one week I had to push her in a wheel chair the the rhuematogist. Thankfully with the antibiotics it was brought under control. However, the treatment is 15 or so years on antibiotics. This greatly concerns me knowing what this will do to her gut. Do you have any other information on long, long term use of antibiotics and how deal with side effects.
    Thanks so much

    • My mother also suffered from Rheumatic fever (hers was due to undiagnosed strept) she was so sick she nearly died. Doctors wanted her to go on heavy steroids and anti biotics. She chose to do apatherapy instead, she gets stung by live bees. Took about two years but thank g-d she is now back to herself. Her doctors are amazed. She lives in israel but im sure would be very happy to speak to you or your daughter and share any info.

  45. Hi, my 4 month baby has swollen gland behind his one ear. We took him to the hospital. The Dr did a sonar and said it is a infection of the gland. Dr prescribed a antibiotic and probiotic. Antibiotics must be taken in the morning and evenings and the probotics in the afternoon. After the first day the gland started to look less swollen, but the next 2 days it started to look more as it looked the first time. Why does the gland not go back to normal?

    • If they have swollen glands. Put a goop amount of extra virgin olive oil on it everyday. You could also use something for the lymph nodes/glands like IMMUNE BOOM.

      • My granddaughter has been diagnosed with “Cyclic Vomiting Syndrome”. She began with this just in the mornings when she would get up at age of 10. She is now 15-1/2 and the doc wanted to do an endoscope but I didn’t want her put to sleep honestly at 10 or 11. This started when she was being bullied at school. I put her in private Christian school but that didn’t help that much. She drinks about 80 ounces of water a day, give or take, I know it’s a lot, since this started and doesn’t eat well at all. She also drinks juices. Soda, etc. When she does decide to eat it’s late afternoon and she I think is afraid to eat because of the sickness. She frowns on all kinds of food. Will only eat now certain kinds usually Mexican and use to love veggies but refuses most now. Pediatrician put her first on Omeprazole a.m. and p.m. and she took for few years then stopped that about a few months ago due to still getting sick on it. She was Vit D depleted at a physical a year or so ago and took Vitamin D then doc said she was fine so we stopped that. She didn’t throw up while taking that. Now she started on Ondansetron ODT 8mg for nausea which 99.9% helps her from being sick in the a.m. She has throw up when taking a vitamin pill so she won’t take vitamins and does not get adequate supply of food to maintain a normal balance for a growing teenager. She is now home schooled and not doing well with that and I’m at a loss as to what to do with this situation. My 8 yr old and 11 yr old grandchildren eat lots better than her. She has sleep problems now over past couple months and I’m scared for her honestly. Please help me with any advise which would be deeply appreciated. She also has been diagnosed with asthma which she isn’t bothered with too often. However, if she gets sick with a cold it’s hard to get her over it, antibiotics is only way always and she’s never been on any Probiotics as I have a hard time getting her to take or eat anything. I am so afraid of what the outcome of all of this will manifest into for this beautiful child. Thank you for any help you may advise us on.

        • I would highly recommend your granddaughter sees a competent psychotherapist who understands the physical effects of stress and anxiety and psychosomatic disorders. Many symptoms (vomiting, nausea) that you describe are explained by severe stress. It is not a cooincidence that the symptoms started while she was being bullied at school. I know because I had very similar symptoms at a similar age and it was all stress related. Unfortunately, no one knew it was stress related at the time, most doctors look for physical causes. I also vomited, had nausea, wouldn’t eat much, was a very picky eater and had sleep problems. Your description of her sounds very familiar. It is surprising what the body can do from stress and anxiety. A good mind body specialist should be able to help, although finding one may not be easy. In the meantime, you can read some books on the subject, look into what can be causing her stress (if she is homeschooled, is there conflict at home for example?) teach her some stress relieveing techniques, take her in nature and help her relax. At a young age it is hard to understand how to relax, but you can guide her. Best of luck!

  46. I have been taking 3 x500 mg. of keflex antibiotics daily since last January. I am on this for life to treat a bacterial infection of the aorta which caused 2 aneurysms in the aorta. About 2 months ago I developed a change in my bowel movements and now feel bloated and sometimes feel nauseated. I am wondering if the antibiotics are causing this.

    • you may want to look at nattonkinase and serrapeptase for your aorta aneurysms. these can help with biofilms. you need to find natural alternatives to any so called lifetime medication.

      sure it can cause that bloating. you should consider taking a probiotic using beadlet or enteric form as long as you are on antibiotic.

    • Where there is inflammation, there is an infection. We could assume that the antibiotics caused dysbiosis so you have an imbalanced flora. One cause of gastritis is h pylori bacteria. It may be that you just need to balance your gut.

      I’d rather take a more broader approach because there is also a possibility that the problem started before the antibiotics but was just simmering. When one is dealing with medical conditions especially in the colon, there is the unknown so maybe a broader approach is more practical

      Here are some things to consider

      I would experiment with varying doses (2g to 30g) of L-glutamine. This helps repair the lining of the colon. I would recommend you put the L-glutamine in water and sip it through out the day. That will keep you colon more bathed in it. For some people, just this has worked wonders.

      I would consider that fungal infection MAY have got out of control also so considering throwing in some Candida Gone into the mix.

      I would take a probiotic with good amount of ACIDOPHILUS and BIFIDUS

      I would take grapefruit seed extract for the colon inflammation

      I would consider taking Apple Cider Vinegar (with mother) in water. The acidic environment can make it more difficult for some microbes to survive.

      See if these improve things.

      Inflammation of colon in general (IBD, Crohns, UC etc) may require more a more heavy approach. Your going to have to experiment. I would consider getting the AMP if less expensive methods aren’t working. Try for 2 months.

      Hopefully this gives you some kind of start

      • I avoid antibiotics at all costs, When I had kidney infection my doctor wrote a presription for antibiotics had I been thinking would of all for IV antibiotics to sAve myself undue suffering

        Anyhow my doctor is super genuis sought after doctor he put me on saccharomyces. boulardll 3 times a day and 15 drops grapefruit seed extract twuce a day I took plus vital 10 probiotic i also drank kefir he told me to avoid sugar. You can also ask the doctor for pharmaceutical grade probiotics which had gazillion cfu
        I believe one day antibiotics will one day be rarely used they will come up with a stronger super probiotic that will play defense,

        • Wow that is so impressive to have a Dr so proactive do you mind sharing the name of your Dr? I am in desparate need of a good one.

    • i used Aloe Muciliginous Polysaccharride capsules to address infections like ulcers and pouches in the colons.

      1 bottle cost $126. It has 270 capsules. I am going to experiment using 7 capsules per week (maybe 2 capsules every 2 days) to protect my colon from infections as a form of maintenance so should nip any infection in the bid. It should last nearly 9 months.

  47. I have a herniated disk and have never heard of anything like that. I would be very reluctant to follow this course. If you have sciatic symptoms I highly recommend Neurontin (Gabapentin)

    • Herniated discs and back problems can be cured with Hyaluronic Acid (at least 3 tablets) on empty stomach. You can take higher dose in first weeks because it accumulates in your body. Use the Biocell version because it absorbs well. It takes 6 weeks to cure it. You will likely notice if it is working within first two weeks or maybe even days.

      So throw the antibiotics and neurontin into the waste basket.
      No need for it.

        • So you actually gave the Biocell HA/Collagen. How many tablets and what brand did you use ? Did you take it on empty stomach. For how long ? Did you get any improvement ?

    • I know the post about the herniated disc is older but for anyone interested this method worked for me to treat my herniated disc. I followed this to a day every day and then went to a clinic to get the next set of “e-sizes” and after two months I was completely healed.


      I have used this book for 15 years, the e-sizes always work for various injuries. I know follow the “final set” every day. I have no pain. Highly recommend.

  48. Hi, the following regime has been recommended for a longstanding back pain problem (modic changes in verbetral bones adjacent to a herniated disc).

    “….one tablet = 500 mg amoxicilin and 125 mg clavulan acid) in a dose of 2 tablets 3 times a day with an 8 hour sequence for 100 days…..”

    This is a massive dose of antibiotic – anyone else used this protocol and been ok on it? Interested in any views.

      • hi sarah, i just came off the exact same antibiotics for a nasty infection in a dental implant i have just had removed. i am taking glycine in the form of great lakes hydrolysed collagen (from iherb), and a probiotic called biokult (which is excellent clinical grade and stable through stomach acid). i have been eating traditionally fermented foods (veges, kombucha, home made yoghurt etc) for years now but make sure to have them several times a day at present. its 3 days since ceasing the metronidazole (which i suspect was causing the bowel inflammation and diahorrea) and i am back to normal today phew!

  49. I am taking Doxycycl HYC 100mg twice a day because of a tick bite. I was looking for probiotics from food to take with this antibiotic. Your article had good info.

    • Here is a collection of things different people are taking using long term antibiotics

      Ultra flora IB
      Ther-Biotic Detoxification Support (Vegan)
      Dr. Ohirra’s “Professional Formula”
      Probiotic (lactobacilli and bifidobacteria)
      Fermented foods such as pickles, sauerkraut, kimchee and miso
      refrigerated bottle of liquid ACIDOPHILUS PRIOBIOTICS 1tbls per day.

      Please be aware that what works for one person may not work for another. It is a trial and error and finding what works for you.

  50. My father is on co amoxiclav and moxifloxacin hcl for his foot wound. he is diabetic and thats why the healing of wound is taking so long, before this prescription he was taking clindamycin, all of these antibiotics are causing quite severe side effects diarrhea, fatique and weakness. what specifically should he use in his diet to improve his condition keeping in mind he is diabetic not allowed to eat lot of sugar

  51. Dear Mr Chris,

    First of all, I would like to appreciate you and this website..which is more helpful for the peoples.who has lack of knowledge on pro-biotic and Pre-biotics.

    I am writing my story to seek you help, Hope you would also help me to overcome my life-threatening situation.

    I was having stomach ache for the past 8 months and before two months, One of gatstro-enterologist found H-Pylori infection during gastroscopy by doing Biopsy.

    Post to that the same Dr Prescribed the H-Pylori antibiotic Kit contains ( Amoxicillin Capsules 500 mg – Thrice a day
    Metronidazoles Tables 400 mg Thrice a day (14 tables), Omeprazole – Thrice a Day ) for 10 days. Which i have completed with horrible side effects, Like nausea, Drowsiness, Stomach pain, Chest Pain, High Wind, Neck and Sholder Pains and more.

    Post i have completed this medicines, I have faced lot of difficulties until now. Continuously being to ER at nearest hospital due to high-Fatigue ( Which i could not do anything and being on bed ) , Stomach pains, full muscle pains, body pains, Urinary Tract infections and Leg pains, Throat pains etc…

    overall my situations is being worst now, I could not able to do anything and could not able to sleep even.

    I recently came to know about this Pro & Pre-biotics and I bought VSL#3 capsules. But not sure whether it would work for me or not.

    Kindly help me and suggest, How to come out of this traggetic situation.

    Awaiting for your valuable reply to save my life.

    • I don’t think Chris will have the time to answer you.

      No doctor will be able to tell you if something will work. Health conditions can be complex especially gut issues. You can have preexisting issues and post issues. You will have to approach it from different angles.

      One angle is to use VLC#3 and see if that helps.

      Next angle is to treat potential infections like fungal.

      Next angle is to introduce fermented foods like kefir.

      Next angle is to research other supplements mentioned in comments and test them.

      It will be a trial and error approach for you like everyone else.

    • You really should get tested for Lyme disease if you have not done so.

      iGenex lab in California is best.

      My wife was undiagnosed Lyme for 8 years and had a myriad of symptoms that could not be explained by the experts. We are just beginning her lyme treatment now. Hoping to put this nightmare behind us.

    • Hi Krishnan, I read your post and I can shed some light on that especially as I am going through the same thing… Gut days biopsies due to antibiotics and amalgam fillings… Do you have any fillings ( which are actually 50% mercury) which are a contributing factor to dysbiosis. You must consider having these removed by a qualified mercury free dentist ! Let me know!!

  52. What a wonderful site, thank you.

    Last night I was prescribed the antobiotic clyndamycin for an infected tonsil, after the er doctor drained most of the pus.

    My question to you is what is the alternative to abtibiotics in this case?

  53. Thank you. I’m going to start her on it today. Also looking into ionic silver water. Wish there was more info available, but I’ve had decent luck with a couple of forums. Know if there is truth to harmful bacteria feeding off of sugar? Baby doesn’t eat much, but if she hasn’t eaten all day I try anything (to prevent nausea from meds) even if that means ice cream.

    • There is a brand of coloidal silver that has been tested and used by the US military. I tried it. It is very potent.

      “American Biotech Labs Silver Biotics 4 oz Scientifically Tested by US Military Hospital”

  54. I have a 16 month old who has had 3 kidney infections in the last 5 months. The first was Pseudomonas aeruginosa and was treated with Cipro. She has VUR, so was put on a daily antibiotic after the Cipro, that was Bactrim. She had 2 e. coli kidney infections while on the Bactrim and those were both treated with Cefdinir. We just found out she has a c. diff infection and was today prescribed with Flagyl. Earlier this week I told her urologist that I do not want to try a new daily preventative antibiotic they are recommending because I suspect that her first treatment of Cipro was what left her so vulnerable to additional infections and I wanted to give her little body a chance to get it’s defenses back up (this was before I found out she has c.diff infection). We took Culterelle during her first round of antibiotics, but I only recently became aware of what gut flora actually is. We just started her on an infant probiotic with 5 different strains, trying to give her sips of Kefir, Kombucha, etc. She hasn’t had an appetite since all of this started, so food is hard. She is pretty much exclusively breast fed at this point. I’m in tears over her being either with infections or on antibiotics. Any advice would help. Interested in s. boulardii perhaps to help treat the c. diff as well as any other ways to help get her gut in the right place. I’ve read mixed info on whether probiotics I ingest will transfer to her through my breast milk.

    • I would experiment with Saccharomyces Boulardii.
      It supposedly has been shown to normalize c diff and h pylori.
      The dosage has to be researched. Different research
      studies used different dosages. It also prevents antibiotic diarrhea. I’d consider taking this if taking antibiotics irregardless.

    • i just read recently that s. boulardii is one of the main bacteria in kombucha. can you dilute it and second ferment with raspberry or something to get her excited about it? my toddler LOVES kombucha.
      I really feel for you. Sally Fallon in recent years has produced a book called i think ‘nourishing traditions book of baby and childcare’ which is excellent. definitely take the fermented foods yourself to benefit her. Also consider high vitamin cod-liver oil and butter oil which contains high vit D for immunity this will be outlined in the book. best wishes from another breastfeeding mama x

      • Love you comment , Cowgirl! High vitamin Cod liver oil and bone broth definitely worth a shot! Also raw cows milk over pasteurized…if you are drinking. Best of luck to you and stay strong!
        Try to seek out a homeopath who can help you find the root cause of her illness.

  55. I am being treated with antibiotics for late stage Lyme Disease. I am taking both supplements that you mentioned in this article. My question is whether you have any advice as to WHEN I take the supplements in relation to the antibiotics. My LLMD advises taking probiotics 1 hour before the antibiotics (or 2 hours afterward). Have you come across anything in your research related to timing of probiotics during antibiotic treatment? Thank you!

  56. Hi there,

    I know probiotics should be taken 2-3hrs away from antibiotics, but what about other supplements like – milk thistle, Glutamine, fibre, etc.

    Thank you

  57. Chris, I hope you still reply to these posts. My 12 year old daughter is in the hospital trying to recover from terrible digestive issues. She is now on a feeding tube because she has become so malnourished.

    She had pneumonia in December 2013. She has scoliosis and we were worried she could not cough up the stuff in her lungs so we allowed the antibiotics. She was almost hosptialized then. She ended up on 2 antibiotics at the same time, Cefdinir and Azithromycin. They also gave her an inhaler, but we only used it 2 times.

    She has suffered from nausea ever since. We did give her high level probiotics afterward, but they had no affect. In March she started eating less because the nausea was getting worse, which in turn caused some constipation and gas which caused less eating. Then acid reflux started. She was put on nexium. Everything snowballed into some gastroparesis and her being in terrible pain. She can verp up undigested food eaten 6 hours earlier.

    We have been to numerous doctors and have had every test known to a GI specialist. They could only confirm that she was terribly constipated and has acid reflux, but her esophagus, stomach, and intestines are in great shape. She had mild resolving gastritis from the acid reflux. And her lg intestines were slightly dialated from the constipation.

    She has lost 17 pounds and refuses to eat much because of the pain. I know she needs the feeding tube now, and it will probably restart her stomach. And with eating, the pain may go away. But the nausea was there before any changes in eating or malnourishement, and I am worried it will remain.

    The doctors are worried it will or has turned into an eating disorder. She is not the type of child who has ever been worried about what others think, very confident and secure in who she is. But when something so primal as eating can make you feel like your guts are being cut out, I don’t know what that can do to your future thoughts of food and fear.

    I have even requested them to test her for Addisons. I have also talked them into doing an ultrasound of her abdomen to see if she could have gallstones. I would appreciate any suggestions. I have spent hundreds of hours doing research and haven’t found the answer yet.

    • Hi Laura,
      I am so sorry. I can imagine how terrifying that would be! I highly recommend you read the GAPS Diet book. I think it will give you some insight into digestion. It was written by a neurologist/nutritionist for her autistic son. It may seem unrelated to what you’re dealing with, but it provides a good template for repairing digestive isssues (which Dr Campbell McBride believes are at the root of autism). It did amazing things for my severely impaired digestion which sent me to the ER with dehydration when I became severely under weight, where I was provided no answers and all tests came back normal. I did my own research and found this diet. Good luck in your search for answers.

    • There seems to be a lot of chronic idiopathic (unknown) nausea out there that people have been carrying around for decades of their lives with no resolution even getting practically all known medical tests.

      Based on that, I would not go down the conventional medical route to resolve the chronic nausea when eating food. Like so many health conditions, it’s clear their not interested in solving it. Sometimes it can be caused by vestibular origin. You have to do your own research and experimentation. I would stay away from pharmaceutical medications.

      Given that the cause seems precipitated by antibiotics, I would suggest looking into introducing fermented products when she gets out of hospitable. First on list would be Kefir Milk. This can heal the digestive tract in many unknown ways.

      Buying commercial Kefir milk is not only expensive but devoid of benefits so you want to find starter kefir grains and do your own homemade version. Even commercial yogurt is devoid of benefits.

      You want to use raw milk. You can use pasteurized milk but they need to be transitioned. I found my kefir milk grains locally by going to a website localharvest.org and calling one of the farms close to me. There may be other sources close by. Finding them locally is better since they don’t get dehydrated during shipping so will be more healthy. I can get raw milk at farmers market on certain days. You need to search for that also.

    • Scoliosis and constipation send up red flags for me to check her thyroid. My daughter has Hashimoto’s (autoimmune thyroiditis) and her main syptoms were both of those. Also, think about testing her for gluten intolerance and its cross reactors with Cyrex labs, maybe the nausea is is linked to food intolerances. Best wishes.

    • Hi Laura,
      Pls look into SIBO ( small intestine bacterial overgrowth).
      I had very similar story as you describe and it was from overuse of antibiotics.
      It is based on some more recent research so not all the docs may be aware of it yet, you just need to find the right one.
      Hope it helps, Petra

  58. Thanks for the info. I’m defrosting my beautiful bone broth right now. Had unexpected root canal and I’m on AMOX/K CLAV 875 mg twice a day for 12 days. I had no choice on as my infection was really bad. I’m drastically increasing my probiotic intake to several times a day, eating more of my homemade fermented foods and raw fermented dairy (yogurt, kefir, cheese, etc.). Dentist knew I was freaking out over taking antibiotics so she prescribed the most gentle (I’m trusting her on this one).

    • I have H pylori and I’ve tried to eradicate it with natural remedies however it has not worked. So I’m going to start taking antibiocs this Friday.

      I made my own bone broth, you mention taking probiotic and prebiotic. I have saccharomyces boulardi and it is ok to mix with the Ressistant Starch and when is it better to take it.

      This are the antibiotics i’m going to take
      Lansoprazole Capsules (Gastro-Resistant) 30 mg (28 Capsules)
      Amoxicillin Capsules 500 mg one to be taken three times a day (21 capsules)
      Metronidazoles Tables 400 mg one to be taken twice a day (14 tables)
      Thanks for your help

  59. I am dealing with type one diabetes chronic fatigue Candida and unresolved thyroid issues, As well as digestive stuff.

    I told my doctor yesterday I was having pain near my left kidney(I thought it was just my adrenals screaming) She did a urine dip, Which came back with pus in my urine at an elevated level. She had them take a culture on it which will be available in three days. She also sent me for an ultrasound, I won’t see the doctor for another week but apparently I have a growth on my bladder.

    Before I left the office to get the ultrasound, She was very firm about me taking Cipro….. whatever that antibiotic is. I would rather wait until at least the culture comes back to see if I really really need it. I don’t feel any worse than I usually feel with all of my other ailments. The doctor was afraid that I would end up in the hospital on IV antibiotics.
    What do you think?? I’m part of the paleo code forum, but not sure how to access. The infection explains why I am so insulin resistant lately. Could the growth explain recent digestive issues? Is there something else I should take, like D-Mannose?

    • DO NOT TAKE CIPRO unless you don’t care about getting ligament and tendon damage. Fluoroquinolones are known to cause this. There are numerous lawsuits, look it up. I’ve had persistent Achilles tendonitis for YEARS as well as shoulder impingement. Reviewing my records shows I was taking these drugs just prior to injury. I’ve gotten to the point that I list these drugs as allergens.

    • As far as kidney pain, it possibly could be kidney stones.

      There are a whole wide range natural remedies if that is the case. Some of those remedies were more complete and addressed infection. I used renavive for that reason. There are a broad spectrum of products and home remedies.

      You didn’t make clear what digestive issues you have.

  60. Great content on your site! I’m taking a long course of Rifaxamin for SIBO (which probably resulted either from a huge antibiotic and steroid hit I took last October for a bacterial infection that lead to epiglottitis + simultaneous strep; bears noting that I got GERD severely after infection and was told to take months of PPI); anyhow… I’m working with a new integrative doc who is more open to newer research; would love to know your recommendations for pre and pro biotics after the Rifaxamin course. Side note that I’ve also suffered from disequilibrium and nausea, body aches, and exhaustion – all of which receeding since rifax and elimination diet; CT Scan and MRI came back clean, but balance tests show loss on right side, which dovetails with my right ear and eye being sensitive to sound/light.

  61. my friend just sent me this article, and i’m so thankful. our family was in a terrible car accident about a month ago which resulted in my daughter having her spleen removed. this accident happened in panama, where we were on an 8 month sabbatical.
    the doctors there assured us that the other immune system organs (liver, bone marrow & lymph nodes) would take over the function of the spleen, and that our daughter would lead a normal healthy life.
    i was in contact with our kaiser pediatrician at that time, and she said the same thing, although she did emphasize the importance of keeping current on vaccines.
    when we got back last week, we were told to meet with an infectious disease doctor at kaiser, and she had a very different perspective. she said that my daughter is at extreme risk for bacterial infections and that she should be on low dose antibiotics (250mg penicillin 2x’s per day) for at least 2 years, and ideally 18 years. she also said that if she gets any fever at all, she should immediately take a dose of levofloxacin, and then go straight to the er for a blood culture. and she said these recommendations are based on research on patients with sickle cell, etc, not trauma induced spleenectomies.
    i feel extremely worried about putting my healthy child on antibiotics for an extended period of time. i’m worried that at the end of it, her immune system will be destroyed by the antibiotics, and that bacteria may develop a resistance.
    i’m researching using probiotics to support her immune system as long as she is on antibiotics. i’m also exploring alternatives to antibiotics. i’d love to hear your thoughts.

    • You should consider dropping your kaiser pediatrician or any physician who recommended vaccines. Vaccines will damage the immune system and set your daughter up for future chronic illness and cancer. It will make the current situation much worse. I hope you understand this. If you don’t, you better get off your ass and do the research on vaccines to inform yourself for your daughters sake.

      Look at the Amish. No vaccines and minimal processed foods = very healthy. Autism is very rare. chronic illness is virtually non existent. They even avoid GMO foods because they seen the devastating effects in their livestock. Removing fluoride from water will help too.

      Penicillin is a narrow spectrum antibiotic so don’t wipe out the gut flora. Narrow spectrum antibiotics are easier on body.

      The broad spectrum kind like levofloxacin are more devastating to gut flora. This increases the risk of fungal infections. doctors miss most fungal infections.

      I don’t want to say what you should do in regard to broad spectrum antibiotic but I think this is where you need to focus on. Removal of the spleen complicates things where you need more knowledgeable advice than me. If it is for a short term, it may be more acceptable.

      I am not against antibiotics but some can be very dangerous or bad effects on the body. You have to weigh the risk and rewards.

      I’d go along with low dose penicillin. People who have high risk of cellulitis infection have done well being on penicillin many years. Many years ago I took minocin for 3 years and had no negative effect on gut. I also experimented taking amoxicillin for 5 months. both are narrow spectrum antibiotics.

      There may be natural herbs in concentrated doses that can replace the antibiotics but that a murky area.

      I’d take any antibiotic with bromelain because it destroys the sheath that bacteria use to create bacteria resistance. Most people who developed antibiotic resistance resolved it with addition of bromelain.

      Being treated by conventional medicine increases the risk of more damage to your child so don’t follow their advice blindly or let them scare you. Find an alternative doctor that you can go to for advice if you can.

      Removal of an organ can end up forcing someone to be more dependent on conventional medicine also. It’s being caught between a big rock and the hard ground.

    • Prioris….so sorry about your daughter. I have been researching some possible natural anti microbial/biofilm disrupters to use on a regular basis that might interest you. These are what I have found:
      monolaurin or Laurcidin
      Grass fed colostrum with lactoferrin
      Thymus extract
      Beta glucan 1/3….I think there may be only one brand that works real well…my chinese medicine doctor carries it
      Prebiotic taken at same time as probiotic (RS taken with s. Boulardi, prescript assist, or other high quality probiotic)

      Hope this helps!

  62. Hi Dr. Kresser. Thank you for your article.

    I’ve had a bad cough for over a week that prevents me from sleeping, so right now I am taking prescription cough syrup and antibiotics (azithromycin).

    I am wondering: should I still take hydrochloric acid (HCL with pepsin) while I am taking this antibiotic? I am worried that the HCL will somehow make the antibiotic ineffective, or that I won’t be able to absorb as much vitamins/medicine if I don’t have enough stomach acid.

    Another, perhaps related issue: I’ve tried two different cough suppressants and they seem to have little or no effect on me. They don’t put me to sleep, and they only do a little bit to suppress any coughs.

  63. Hi Chris, thanks for all the great info. I am a huge fan of both your website and your book. My question involves the timing of the probiotic. I typically take prescript-assist with my meals; the antibiotic that I was prescribed should also be taken with a meal. Is this ok, or should I take the probiotic at a different time? Thanks in advance.

  64. Thanks for putting this information out there. I need to start antibiotics today for strep throat and want to minimize the damage.

  65. I can’t thank you enough for all your articles and time. I don’t think you will ever know the full reach of your work and how many people you have helped. Thank you for everything you’ve done to help me without even knowing it. I am forever grateful.

  66. My baby suffers from vesicoureteral reflux and was on a daily small dose of antibiotics since he was 5 days old.(to protect from possible urinary tracts) We stopped the antibiotics when he was 12 months old (today he is 18 months old) but the doctor prescribed no probiotics or anything to protect the gut after the treatment and I myself was unaware that anything like that was necessary until I started reading some articles in the internet. Do you think that the baby should take any prebiotics or probiotics(don t knowthe duifference) now or is it too late and whatever is done is done? Pls note also that the baby has been breastfed and is still breastfed until today. Pls help and thank you for your valuabke time in advance

  67. I have to be on IV antibiotics during labor, which I’m a bit nervouse about. Can you recommend any specific regimen to take before/during/after to keep myself and my newborn from having too many issues? I plan to breastfeed as well and worry about antibiotics passing through the milk.

    • I would think about taking coconut oil before and after. It will keep the many bad guys in check from getting out of control. Start off with small amount and work way up to 2-3 tablespoons. I think antibiotics can set off all sorts of fungus diseases – one of the most ignored group of infections out there.

  68. Thank you for this article, it’s very informative.
    After a case of Rheumatic Fever this past summer, the specialists have said I will be on antibiotics for 5 years…I tried taking probiotics but they made me sick. So now I just drink a probiotic yogurt daily which I’m sure is not enough. I’m also pregnant now (11 weeks). Do you have any suggestions as to what I can take to keep my body healthy? Thank you so much!

    • i assume you are on low dose penicillin. i recall studies of people with cellulitis infections fared pretty well many years on penicillin. You should look at what happens to people on penicillin that long to understand what you may have to do.

  69. Hey,
    Great article as always. I took bio-kult (I’m on GAPS), but I am now on PA. I can’t find any information about the best time to take probiotics, PA. With food or without? Read about probiotics not surviving the hcl in the stomach if taken on an empty stomch. Is this true? Does timing even matter?

  70. For those of you looking for a probiotic to give infants, believe it or not, Gerber has a good option. Gerber recently bought the company Bio Gaia (who made a very expensive probiotic for infants) and Gerber has basically relabeled the BioGaia probiotics as their own!
    The product is called “Gerber Soothe Colic Drops.” They are over the counter and approved for use in infants.

  71. What about someone having a kidney transplant? There are more restrictions on what they can and can’t take, what would you suggest for them to protect if antibiotics needed? For the last 6 months they have been eating 2 big mouthfuls of fermented kraut and kimchi daily. Thanks!

  72. After a long hard battle with a severe ear infection, we finally ended up having to give our 10 month old son antibiotic injections. It has been stressful and very disappointing to say the least. We first tried seeing a naturopathic doctor, tried waiting it out–but the infection continued to progress and was causing 103 degree fevers. It got a little scary.

    I currently give him Pharmax HLC Mindlinx, plus cod liver oil. Is there anything else I can do to repopulate his gut? He is still primarily breastfed but we do give him soft meats, cooked vegetables, poi, and some fruits (no grains, no dairy so far). I was thinking of starting raw kefir (cow), and maybe seeing if he would eat raw sauerkraut, etc. What would you do for Sophie if she ever ended on a course of antibiotics? With babies, there are less food options to offer them until they start eating more.

    • Hi N Boyd,
      I know you asked Chris, but I figured I’d chime in too. We have three kids. Our second and third started on bone broths and milk kefir before a year. And sauerkraut is a great idea too. Both girls (2 and 3) love sauerkraut, salt brine pickles and beet kvass. I think starting them so young really helped.
      Also, FCLO and grass fed gelatin.
      Don’t get too discouraged. It sounds like you’re doing all the right things. If you continue on this path, you’ll be surprised at how much you can repair. When I was pregnant with my first (who is now 6), I ate mostly vegetarian and had horrible gut flora (but didn’t know it). He is so wonderfully healthy and hasn’t taken an antibiotic for 5 years.
      You may want to check out Oregano essential oil as an alternative to antibiotics for the future.

  73. Chris, I love all of your articles . . . and I used to be a big fan of Milk thistle – used it effictively for years during cleaning fasts. However an ND told me last year that milk thistle is now recognized as only beneficial for protecting the liver from long-term damage, and not beneficial for short term liver cleansing. Does that sound right?

  74. I was diagnosed with strep throat 5 days ago and prescribed amoxicillin. I hate taking antibiotics and have only been taking 1-2 per day, as opposed to the recommended 3/day. I caught hell this morning from some coworkers, one of which who called me selfish for not taking my meds as prescribed and possibly putting the rest of them at risk. The other one told me that I need to be careful because strep can affect my heart. I feel fine, haven’t had a fever since Friday, my sore throat is gone, and I feel otherwise healthy (aside from a very slightly stuffy nose). Is there any kind of middle ground with antibiotics, where I am receiving the strep-fighting benefits but not wreaking as much of havoc on my gut? I felt ill-prepared with my rebuttal and really should have just kept my mouth shut.

    • There are views that state that taking antibiotics for strep throat are useless. It doesn’t make any difference in recovery. What many people have done is just let the strep throat clear itself. I did get strep throat a year ago and took amoxicillin but on hindsight I wouldn’t take them again. My inner sense says that they made no difference.

      As far as people’s reaction, you have to understand the standard advice. I don’t think a short term stint on amoxicillin is going to harm you so I’d compromise and either take the antibiotic or just plain lie and tell them you are taking it so there are no political problems and for their psychological comfort.

      I do think strep is communicable so you shouldn’t go to work if you are still sick. If you are well then I wouldn’t worry about it. Maybe just wash your hands during day at work for a week or so as a safety precaution since you are more likely to spread it by touch.

  75. Are the above mentioned prebiotics and probiotics safe in children who are prescribed antibiotics? My 11 month old is battling yet another ear infection and I’m beyond reluctant to utilize antibiotics without some natural assistance. Any help is greatly appreciated.

  76. Chris, do you have any information about the effects of a colonoscopy (specifically, the colonoscopy prep) on the gut microbiota? Is it as devastating to the gut flora as antibiotics? It has been 10 years since my last screening colonoscopy, and my doctor has been bugging me to schedule another. I have a reasonably happy gut at the moment, after a certain amount of effort with careful diet, probiotics, fermented foods, resistant starches, etc., and I hate to think of it all going down the drain, so to speak. I assume that your tips for antibiotic use would apply to any disturbance from a colonoscopy. Any other suggestions?

  77. My seven month old son keeps getting ear infections and we are trying to avoid antibiotics but are now on our second round in a month. If I take a probiotic and/or prebiotic will any of the benefits be transferred to my son if I am breast feeding? I’ve seen Culturelle for kids but it is recommended for age one and up.

    • Valerie, try breast milk directly in your little one’s ear to help with healing. I also gave my child both Bio Gaia Probiotic Drops and Baby’s Jarro-Dophilus before she was one.

    • Middle Ear Infections

      “90% of upper respiratory infections, including children’s ear infections, are viral, and antibiotics don’t treat viral infection. More than 40% of about 50 million prescriptions for antibiotics each year in physicians’ offices were inappropriate.” CDC

      “I have treated many hundreds perhaps thousands of cases of ear infections with echinacea and I know it works. I rarely have to give antibiotics or use tubes to clear up these infections.” Doctor Jay Gordon, Pediatrician Cedars Sinai MC

      “The best way to prevent allergy in infants is to breast feed them. Children who are allergic to foods often have fluids in the ear tube leading to infections.” Prevention

      “We found in our clinical practice an over 90% reduction in middle ear problems with the kids using xylitol for their teeth.” Doctor Lon Jones D.O. Note Doctor Jones also had good results using xylitol with colds, allergies, ear infections, sinus infections and dental health.

      “I hope with the publication of this book more pediatricians will get their earache patients using xylitol.” Doctor Lon Jones D.O.

      Giving a child Drug Antibiotics for a middle ear infection is almost never a good idea. Anti-biotics are vastly over prescribed presumably to induce the placebo effect in the paying stiff. Fine, use SUGAR PILLS, please. Believe it or not Drug Anti-biotics are STILL given for viruses. But please don’t YOU be so foolish as to accept this insane “Prescription”.


      • Fungal infections are the most under reported infection around. They are implicated in COPD, emphysema, bronchitis, asthma, sinusitis etc. People who have cured themselves used an anti-fungal approach.

  78. Hi,

    This is a great article. I am so excited to see this! I have been considering Prescript Assist for several months, but have been hesitant because I’ve read some warnings against it because the SBOs are spore-forming, and apparently, they can take over and cause problems because of this. I am wondering what Chris Kresser’s response is to this.. AND… feedback from anyone else who has tried it.


  79. I’ve been drinking a mass-produced kombucha available at grocers – I would appreciate any feedback on whether or not it is worthwhile from a gut flora perspective , or just a marketing gimmick?

    • Some people have chosen to not take Kombucha due to the high flouride content. Some have changed to Kefir soda. Suppose to taste like cream soda. You can make your own. Kefir is a very good probiotic also.

      I haven’t looked into the issue too much but one needs to distinquish between natural fluoride and synthetic fluoride (for lack of a better term). One perspective is that natural fluoride is beneficial to the body.

      My only position on fluoride is that the kind in water supply damages ones health but I haven’t done enough research to decide about Konbucha.

      These are the things you need to look into.

    • Up until a few years ago commercial kombucha was umpasteurized. If I’m not mistaken the feds started requiring that it be pasteurized, so I assume it has no live bugs left in it. (I know that live cultures are ADDED BACK to yogurt and kefire after the pasteurization, I don’t think this is the case for commercial kmobucha). Maybe somebody can confirm this for us.

      • Best to make your own. Avoid commercial products. Use raw milk if you can. The reason raw milk was banned was to increase death and disablement in the population.

        Pasteurization is acceptable if your going to boil or cook the milk.

      • Do they not impact the gut flora at all? I’ve heard that side effects are not as bad, but since they are running through the bloodstream, wouldn’t they still have some effect? I’m actually not sure, but wanted to get more feedback.

        • Chris Kresser should give the definitive answer.

          i found this comment by someone
          Its the route out that counts.
          Some like IV vanco will be filtered by the kidneys and peed out and not reach a “theraputic” level in the gut
          Others like IV flagyl will be filtered by the liver and be excreated in faeces meaning the gut gets a “theraputic” dose of antibiotics.

          I would think the antibiotic would be more diluted if it goes through the body hence less impact on the gut if any does and up there

          • Chris Kresser, could you comment on this one? What effect do IV antibiotics have on gut flora verses oral antibiotics?


  80. I have had constipation for almost 70 years. I have an artificial aortic valve and take coumadin. Any time I need dental work I have to take a three pill antibiotic all at once. I am suspicious that I severely lack bowel motility. Right now I take a heaping Tbsp of ionic citrate of magnesiun, nightly. That keeps me pretty regular and I do drink 70 oz of water every day. I do Crossfit four days a week, eat Paleo. Any suggestions? I have used the prebiotics and probotics but do not notice any change. My CF coach suggested some sort of fresh, liquid p. biotics but I can’t find any. Help!

    • Coumadin is a very bad drug to be on. It is one of the four drugs responsible for 25% of visits to emergency. It causes damage to ones health in long run. It is better to take nattokinase which has no side effects.

      • I have been writing down the suggestions and looking up all the ideas. I only need the antibiotics when I see the dentist, for instance. The concern is not to let clots form on the artificial valve. I was thinking that needing them several times a year was interfering with the natural biota in the colon.
        Thanks for all the ideas, I will post when I try one or several with the results.

    • Sally,

      google up Resistant Starch. I believe Chris has covered this somewhere, and there’s oodles of rather uncouth, but amusing and useful, information over at FreetheAnimal. I tried it and it worked like a charm in about a week. Main advice would be to start veeeery slowly and up the dose gradually.

  81. When you say “beneficial bacteria is found in … peeled fruits” do you mean fruits with edible peels or do you mean fruits from which you have removed the peel.

  82. I recently had a baby and had to have a c-section due to placenta previa. I took sacc. b, Prescript Assist, and FemDophilus double doses daily for a week afterwards. I also stored my fecal microbiome in the freezer to transplant back to myself afterwards. 8 months later it’s still in the freezer, hehe! I think we should all store our microbiome in the freezer every 6 months or so just in case of an emergency where we would need antibiotics. I also an an organic gardener and made a point during and after pregnancy to sample some compost, and my baby loves to do the same.

    My baby got HLC Neonate the day he was born. So far so good, no autoimmune stuff like older sibling was showing soon after birth.

    Thanks again Chris, you have really helped me to have a healthy pregnancy and baby.

  83. Always interesting to read your articles. Thank you.
    I was wondering what you thought of the Klaire Labs brand (Biotagen) for probiotics and prebiotics ?

    • Biotagen is a good prebiotic that I use in my practice. Klaire makes a number of probiotics. I use their Therbiotic Infant with kids under 2 years old, but I prefer Prescript Assist for adults.

  84. Thanks for another informative article, Chris!

    Just curious…if you recommend potato starch for resistant starch, why can’t one just eat potatoes? Is it due to the saponins (which I believe are largely concentrated in the skin)? Would potato starch have saponins?

    Again, thank you for all of the info!

    • Potatoes that have been cooked and then cooled for 24 hours contain resistant starch, but I think the resistant starch is degraded as soon as you heat them up again. So I think eating 24-hour cooled potatoes is an option for RS, as long as you like cold potatoes! (Potato salad, perhaps?) Not sure how much RS is in a potato though, compared with the potato starch.

      Along the same lines, be sure your potato starch is unmodified, and don’t heat it. Otherwise, it probably won’t contain RS.

  85. This article is very helpful. Thanks for the pro biotic recommendations.

    I thought I would add that many people use Oregano oil as an alternative to antibiotics. No one in out family of 5 (ages 35, 34, 6, 4 and 1) has needed an antibiotic in 6 years. We use therapeutic grade Oil of Oregano (usually topically and if serious internally) for everything that would normally require antibiotics. I have cured numerous bouts of mastitis with Oregano oil. Oregano is also an antifungal, which kills Candida, so yeast overgrowth doesn’t tend to occur as it does in antibiotics. There are numerous studies on PubMed.

    • Good to know, Megan. Do you have any recommendations for using the oil for ear infections? My kids are 10 months and 3 (twins) and they all recently had ear infections for the very first time. The inner ear was infected, so I’ve heard that drops or anything put into the ear doesn’t reach that part. Do you know what to do in this case? They all had Amoxicillin and I hated giving them antibiotics, especially the baby. What are some other uses for Oregano in order to avoid antibiotics? How did you use it with mastitis? Topically? Internally? Thanks!

      • For children with ear aches, you can get immediate results with the help of a classical homeopath. I’d also see the comments above for probiotics for children.

        • Thanks Megan and Beth! I just recently started purchasing Young Living Essential Oils. Oregano will be my next! We do a lot of bone broths and probiotic foods too. I have an appointment with our nutritionist this Friday to help get recommendations specifically for infants.

          Megan, is the Melrose Oil good for fighting infections? I’ve heard of using Oregano, but I don’t know much about Melrose. I am fairly new to using essential oils. Does rubbing it on the skin still have a pretty powerful effect internally?

          Thanks again!

          • Hi again Christine 🙂
            Yes, I do find that most often applying them topically is enough. They are very powerful.
            Melrose is a blend of Tea tree, rosemary and clove (maybe more- I can’t recall). And Oregano would work behind the ear as well.
            Good luck finding answers.

      • Hi Christine,

        We do a lot of what the articles says already- bone broths and tons of probiotic foods as our base. I am a minimal interventionist, so I prefer to let things play out on their own or treat them minimally. On myself and kids, i usually use essential oils topically. I do use them internally, if I feel it necessary.

        My experience with ear infections is rather limited. I think between my three kids, we’ve only dealt with ear infections 5 times, so I wouldn’t say I’m an expert or anything. I do consider it a success that none of them has ever taken an antibiotic for an ear infection. When they are very young and breastfeeding I squirt breastmilk in their ears. I have also used ear oil (garlic, mullein, thyme and tea tree) in the ear canal. I rub Young Living’s Melrose blend behind their ears at the first sign of infection and then 2-3 times daily for 3 days after symptoms resolve. I also rub Oregano oil diluted 1:4 with olive oil on their feet.

        If I want to give my children an oil internally (I use Thieves blend), I make a paste with honey and powdered slippery elm and then add 2 drops eo to each “lozenge.” Or I simply put a drop of eo on a spoonful of honey.

        For mastitis, I apply tangerine, geranium and oregano topically to my breasts. If the mastitis seems to be getting away from me, I take oregano internally- just a few drops under my tongue, 2-3 times daily.

        I have used it with success on my dog who had an infected bag of fluid on his neck that the Vet lanced and then prescribed an antibiotic for. I gave the puppy one dose which he vomited up and then decided to use Oregano. I gave it to him diluted in capsules for 2 weeks and he healed completely. I have used it for my sick chickens as well. It really is incredible.

        The reason, I started using essential oils was to treat persistent thrush/Candida that not even rx antifungals would kill- but Oregano oil did. The thrush came on after I took an antibiotic for mastitis just after the birth of my first son. I have had mastitis at least 6 times since (because of my tendency towards oversupply) and have always used Oregano with success. Although it is comparable to a broad spectrum antibiotic, I personally feel that it is far less damaging to gut flora. I have not experienced any ill effects and I’m pretty aware of my body. Hope this helps.

  86. Thanks for the info! My baby (10 months) is on Amoxicillin for a severe ear infection. We did everything we could to avoid it. We waited to see if she could clear it herself, and used red light therapy on her ear. It spread to the other ear and she started losing weight, so we had to do it. I HATE that her perfect little belly is now ruined. She used to be the happiest baby in the world and now she won’t sleep, and fusses all day. I think her ears are better, so I don’t think the fussiness is from pain. I know the link between digestive health and the brain, so I’m worried this has effected her personality.

    We spent a long time fixing my 3 year old twins’ digestive systems due to prematurity (which resulted in food allergies/damaged gut lining) and I really don’t want to go through all that again with her.

    She still breast feeds and I plan to for a long time. If I eat the fermented foods, does that translate into the breast milk for her? I am giving her an infant probiotic but it does not have S. boulardii. Is S. boulardii safe to give her? Also, I’ve heard soil based probiotics can be dangerous for some people. Any thoughts on this? Should I/she take them? We’ve used Prescript Assist before for my 3 year olds, but that was before I heard about the possible negative effects.

    Any suggestions for babies?? Please help!! (Btw, my 3 year olds were on Amoxicillin too for the same reason, but I’m more worried about the baby’s digestive health at the moment. I suppose I could do for them what I do for the baby).

  87. I’ve just landed in bed with what appears to be the flu. Home remedies that REALLY work please? I hate taking medicine, and obviously flu shots.

    • Salt-water gargles for the throat. Tylenol for muscle aches, but no more than 3000 mg per day, (assuming you’re not allergic to Tylenol). Lots of chicken soup, hopefully made with bone broth. Lots of fluids in general. As much rest as you can get.

      If your temp drops after a few days, then a few days later rises steeply, plus you’re feeling short of breath, consider this: one of the worst complications of flu is bacterial pneumonia following in the wake of the virus. Time to see your doc.

  88. I recently was started on triple antibiotic therapy (to continue for a minimum of 3 years ) for a Mycobacterial lung infection. Unfortunately because I have chronic SIBO I have avoided probiotics in general. Do you know if there is a good probiotic choice for me that would be helpful in preventing antibiotic associated diarrhea or Cdiff but will not exacerbate the SIBO?

    • I have some knowledge – by way of experience – with what many of you are asking, as to all of these conditions – and for which most are representative of the untoward (not good) side effects of antibiotic interventions.

      Antibiotics can – and do – “Save Lives” – depending upon the type of infection. If, for example – you suffer a puncture wound, where pathogens are directly introduced into the body – antibiotics are your best answer to prevent – or abort an infection. However, and that being said – the same does not apply to a waterborne – or food borne infection – because here – it is “once again” about biological terrain management, and by way of example – ‘fully one third of all gastrointestinal poisonings are “Viral” and taking an antibiotic – will whack the Immune System – and could lead to death.
      Any overgrowth… whether SBIO – or otherwise – is an ‘Imbalance of Biological Terrain Management – and the singular best response is Prescript-Assist. OH… and I am speaking as Flight Crew Member to the World’s largest Airline… for which I fly ‘exclusively’ to foreign Countries – and for all of us who use P-A (as it is fondly called) – maybe thinking of a Physician Assistant… or Prescription Assistant – we ‘never’ have gut issues – while eating and drinking ‘just about anything’…. Oh Yes… .we may experience a little diarrhea, if we eat something that is quite contrary – but all we do, is to take a few more P-A – and as we say: “Be On Our Way”…. and that is “Not to the Hospital” – but Back to Work.

      Remember: Crowd Out the Pathogen, Consume the Food of the Pathogen, Consume the Pathogen for Food – or emit a metabolite – to Control the Pathogen… End of Story!

    • Yes, Prescript-Assist is safe to take with SIBO which is one reason I recommend it. The same can’t be said for lactic-acid probiotics like acidophilus.

  89. Thanks, Chris–it is great to know that when you take antibiotics all is not lost if you take probiotics. This is the first time I have actually seen this in writing anywhere and I won’t get as stressed out next time I need to take antibiotics–usually for a bladder infection.

    • Joyce, while all is not lost probiotics and prebiotics do not restore the microbiota to the same state it was in before antibiotics. They are a way to mitigate the harm, not erase it. So it’s still wise to avoid them whenever possible, and only take them when necessary.

  90. After learning, couple of years ago, about the devastating effects of antibiotics, I kept asking myself how did I end up having such a healthy digestive system (and good overall health), no intolerances or allergies ever. Growing up in Eastern Europe in the 80’-90’s, I used to take at least two rounds of antibiotics per year, usually more, prescribed by my doctor for sore throat infections. I even took some kind of antibiotic shots (very painful) for about 3 years on and of, at age of 10, for “preventative measures”. Antibiotics are sold over the counter there and people are popping them as candy for simple colds and coughs, even thinking that it’s straightens they’re immune system.
    After reading your article, I now have an idea: we grew all our vegetables, and during the spring and summer I used to play almost every day in the garden and snack on whatever was growing, green apples, peas, tomatoes, carrots, without washing them of course. We consumed lots of pickled vegetables, tubers, yogurt, broths and some kind of fermented drink, similar with kombucha, all of them homemade of course.
    About 8 months ago, being pregnant I had to take antibiotics for a massive tooth abscess. My now 6 month old daughter, has cradle cap and eczema flair ups, recurring colds also a big red spot at the crease of her neck that would not go away with over the counter anti-fungal cream (recommended by her pediatrician).
    I recently learned that it might be due to antibiotic use during the pregnancy.
    I would love your opinion on this.

    • Therbiotic Infant from Klaire Labs if they’re under 2 years old. Same recommendations in this article if over 2 years old.

      • Hi
        I’ve been on antibiotics for 9 years treating rosacea, I recently found out I have candida and some serious bad bacteria going on. I’ve stopped my antibiotics for the rosacea as I’m treating the candida at the moment with and intense diet. My rosacea is back and it’s so bad 🙁 I’ve tried creams they don’t work, what if I need to go back on antibiotics, will I still be able to get my insides good again ?

  91. Chris,

    Great book!

    As far as Pre-Script, it would have been my first choice, but the ingredient label states it “contains a proprietary blend of Leonardite and the following microorganisms…” I have yet to convince myself of the safety of Leonardite (humic acid, or more accurately, up to 90% humic acid). Fulvic acids are a particular type of humic acids; see here for an article on the safety — or lack thereof — of fulvic acid:

    Any thoughts on this?

    Thanks and keep up the great work!


    • What you have been told about ‘many things’ – is only to Educate YOU – To the Degree “Someone Else” wants You to Know!
      Leonardite – named as such, is really “Lignite” – the Ore Structure which is ‘above’ Coal – but fondly named after the N. Dakota University professor Dr. Leonardite – who conducted a small library of research on this Miraculous “Ore” structure.

      As far as Prescript-Assist is concerned – this “Carbon-based Mineral Complex” is the Prebiotic Food Source – providing a readily available food source to the broad spectrum of microorganisms in P-A. Why is this significant? To balance – or ‘regain’ the high ground in the “biological terrain management’ – for to maintain, or re-establish ‘homeostasis’ one of four things must occur – to prevent a “Pathogen” from Taking Over.
      1) Multiply fast enough (called Binary-fission, as to make two organisms, from one) to “Crowd Out” the Pathogen.
      2) During multiplication – there is the necessity to consume ‘food’ – and if the microbes consume the food of the Pathogen – it cannot proliferate.
      3) During Proliferation – and in consuming surrounding food sources… often the Pathogen will be Consumed… and thus – will no longer be controlling the Biological Terrain.
      4) Emit a “metabolite” – or antibiotic – AKA Myco-toxin… which will kill / control (inhibit the further growth) of the Pathogen…. Look Up the Story of “NYSTATIN” – as to how the Streptomyces noursei bacteria came into medicine.

      Other probiotics lack these four ‘basic’ functionality principles – and thus are not even in the Same Galaxy – as is P-A… and yet, Leonardite is important for other factors, as it is a ‘natural chelating agent agent… as it’s heavy metals (if present) are “bound” and will not be absorbed by the body – but as to the contrary – they bind with other heavy metals and transport then from the body. Do your research, and you will substantiate these facts for yourself – and then you will have answers supportive as to why P – A is the World Class Probiotic – Prebiotic, that it is… Bar None!

      When you think – or see – Prescript-Assist…. think “Biological Terrain Management” – and with this comes Harmonization of Gastrointestinal Function.

      • Did you read the link I sent? Because you didn’t respond to any of the issues raised in it. The question is still open to an answer with supporting evidence.

  92. Dear Chris,
    I am a 53 y/o otherwise healthy woman who has been eating paleo for one year. Hip replacement surgery infection at incision site has caused me to be on oral cipro and massive doses IV Vancomycin for six weeks. Side effects are joint swelling, soreness and unusually slow recovery time. Wondering if you had any further suggestions?

    • Cipro is a fluoroquinolone antibiotic and for some who are genetically susceptible can cause major health problems. Google search for floxies, check out Dr. Jess Armine’s site. He works with floxies a lot. Hope you find some help 🙂

  93. I am taking massive doses of antibiotics currently 1,500 twice a day, for 2 weeks for H pylori. I was reluctant to take them but was told that H pylori can lead to stomach cancer. Have been on GERD med for +10 years, doc wants me off it. I have had no issues with my gut, thankfully. Am I just one of the lucky ones or is my gut compromised and I just don’t know it? Thank you for the information on prebiotics. I take neither pre nor pro but was thinking of starting to take the pro. However, I will research your website for more details and likely change that idea to the prebiotics.

    • If you are taking proton pump inhibitors they reduce the acid, obviously, but that can lead to B12 deficiency and allow bacteria that the acid would kill to have a chance to take hold – H.pylori is the prime example. I have had a few clients with this same issue and they take deglycyrrhizinated licorice, zinc carnosine, aloe vera and L-glutamine for the H.Pylori. For the acid reflux, I would check with someone who does visceral manipulation to help pull down your stomach – if you have a hiatal hernia. Then I would drink Kombucha or apple cider vinegar and eat sauerkraut along with the bone broth. Home brewed is best because pasteurization destroys the health benefits.

    • GERD is caused by bacterial imbalance (SIBO) in the guy and sometimes H. Pylori infection as well. You have to starve out the bad bacteria. Apple cider vinegar and all the other “natural cures” some people recommended to you never worked for me. What does work is the Fast Tract digestion diet, which involves limited the amount of fermentable (gas-causing) foods you eat. More information here: http://digestivehealthinstitute.org/2012/08/17/sibo-diet-and-digestive-health/

  94. Interesting studies. Thanks for providing the links. I’ve been treating chronic Lyme disease and other systemic infections for several years with herbal and nutritional support. Although I didn’t want to, in the last few months I found it necessary to start taking oral antibiotics and now on daily IV antibiotics as well. Surprisingly, my digestion and bowels have been better and more normal than they’ve been in a long time. I’ve found that probiotic supplements along with a good variety of fermented and cultured foods like you mention has benefited me the most, even while taking so many antibiotics. I think the best you can do while on antibiotics is to take supplemental probiotics spaced out as far away from the antibiotics as possible and try to get some type of fermented foods all throughout the day, even if only in small amounts. Klaire Labs Therbiotic Complete, Florastor, and foods like beet kvass, pickles, sauerkraut, yogurt, kefir and kombucha have helped me quite a bit.

  95. Chris,

    Great article. I am suffering from Lyme disease and have been cycling on and off antibiotics for over a year. Do you have any advice in terms of timing for both prebiotics or probiotics (on a daily basis)? Some protocols have me taking antibiotics 3 times a day so it becomes increasingly difficult to space out 5 pills (assuming I am taking probiotics twice) and potentially 6 pills/mixes if I intoduce a prebiotic into the mix (which I will do per your advice). At this point does timing make much of a difference? Finally, I have been following your auto-immune protocol would the potato starch as a prebiotic be a bad call to introduce at this point? Basically should I just go with the Prebiogen? Thanks for all the great work. You have been a life saver. Looking forward to starting your new book. Best of luck with everything.



  96. Hi Cris,

    I am from Slovakia (in the middle of europe). We call here potato starch solamyl as well. According to you it is solamyl safe and appropriate source of rezistant starch. What is your opinion. Thanks in advance.

  97. My cat, Moccasin, recently had to have antibiotics, and I hated to give them to her and ruin her little gut, but it was necessary in her situation. However, I have done some cursory research online, and found that pets can have probiotics, too.

    I opened up a capsule of acidophilus and sprinkled some on her wet food, and I also gave her a little full-fat plain Greek yogurt. Do you think pets on antibiotics could also have prebiotics? Do you have any pets, Chris?

    • Tarah, Google: Are cat probiotics the same as human probiotics. My understanding is that cats microbiome is populated with different strains than humans so human probiotics may not be the best. I found an article by Dr. Becker on Dr. Mercola’s site that stipulates that. Indeed when I’ve had probiotics sent home with my cat I did not recognize the strains from the zillions of probiotics I’ve take over the years. My vet told me not to use human probiotics for the cat. Additionally it is my understanding that dairy products are not good for cats either as they are intolerant not having the ability to break down milk ‘sugar’. Lactose.

      • Yogurt does not have much lactose and I give my cats some regularly with no ill effects. I have even seen cheese and dried milk on the labels of some cat foods.

        • Just because a manufacturer puts that into a product, doesn’t guarantee it’s good for cats. Sometimes ingredients are included to seduce the buyer of the cat food, not the cat. Just sayin . . .

    • Wellness cat kibble is sprayed down with probiotic bacteria. 80 million colony forming units/pound. Check out the information on the bag. At the beginning, just give the cat a little of this because it may cause loose stools. One of my cats is presently on a 42 day course of doxycycline for mycoplasma. He gets live culture yoghurt every day as well. No diarrhoea.

  98. Your website is informative and I enjoy it very much. However, it is reading my iPad mobile signal and automatically giving me the mobile content rather than the desktop version I would prefer for the iPad. It would be a wonderful improvement if you could offer the choice of either mobile or desktop content on the website rather than an automatic load (and I would have posted this somewhere else, but there does not appear to be another way to contact you). Thanks.

    • Heather, I’m glad you like the site. Unlike some sites that offer a more minimal mobile experience, we are currently loading all of the content on the site regardless of your screen size. That said, given the more limited space on mobile devices, we have to make some layout adjustments as the screen size decreases. One suggestion for you would be to flip the orientation of your iPad. If you view the site in landscape mode (instead of portrait) it will look almost identical to what it would on a desktop. Let me know if that helps!

      • I have been viewing it in landscape and ever since I posted a comment it no longer gives me the sidebar information (popular or recent posts, etc.). Now I have to scroll to the end of articles to see that. Also, I can no longer see the website header, just the article title. Maybe it is just an “error in chair” situation, but I can’t figure out how to get the content to show up in safari the way it did previously.

  99. Is stock the same thing as broth? We get boxes of “Swanson 100% Natural Beef Broth” where the primary ingredient is “beef stock”. I’m sure homemade is much better, but is this stuff at least in the ballpark? It says that it’s fat free, which doesn’t inspire confidence…

    Also, your “getting your hands dirty” link points to http://www.apple.com. I guess you’re an Android fan? 🙂

    • We’ll fix the link, thanks.

      Unfortunately store-bought broth is not remotely the same as homemade, largely because the benefits of stock are primarily in the fat and from the bones, skin, cartilage it’s cooked with. You can add gelatin to store-bought broth to make it more nutritious, but homemade is much better. The good news is it’s fairly easy to make.

        • You can buy really nice broth at the store that is just as good as the homemade stuff. I’ve seen some at my local health food store that even contains gelatin. Unfortunately, they cost like $6 per quart. 3lbs of grass fed beef bones costs about that and you can make maybe 10 qts of broth from it, if not more.

        • Anthony,
          Making your own bone broth is really incredibly easy. All you need is a crock pot (slow cooker) and a chicken carcass. After you eat your roasted chicken, take the carcass and toss it in the slow cooker. Add all sorts of chopped veggies to it, especially onion, carrots, celery, add a bay leaf and some whole black peppercorns, a little sea salt, and cover it all with filtered water. Set the cooker on low for 12 hours. Turn it off, allow to cool for a few hours, then strain. Voila! you have bone broth. The color is magnificent. No store-bought stock/broth will ever come close to the richness and delicious flavor of homemade. Give it a try.

          • Thanks. Maybe I’ll give this a try. I had read recipes saying to cook for 24-48 hours on the stovetop, which sounds like a hassle and I don’t like the idea of leaving the stove on for that long; the crockpot seems much more appealing for this. I’m more interested in beef broth than chicken broth, though; I wonder if just 12 hours would be sufficient for beef bones?

            • 12 hours would be enough for beef bones. For beef you are supposed to roast them a bit first, but I’ve done it without roasting. When you buy the bones (preferable grass fed bones) you want to get joint bones that have some cartilage in the so you will get the nice gel from it. If you can let it go more than 12 hours, that’s good too. You will see the meat and cartilage come off the bones and that means it’s done.

              • I would recommend 3 days on the beef broth! 12 hours is not even enough time for chicken broth. A very low boil is all that is needed. Do not forget to skim the scum off the too in the beginning.

          • That’s a great solution – I stopped carbs and most importantly SUGAR about 5 months ago. Enormous changes, dropped 40 lbs like it was nothing, which was not even the point – no longer get every cold that comes along. I have found that planning to be hungry is an important part of this program – a little forethought and planning. So now, each week, we get a roasted chicken at Costco (as we always did), and when it’s done, do exactly as you recommended, and put away the bone broth in the freezer, so it’s available for soups. Silly to just throw away a perfectly good carcass!

        • Wise Choice Market makes bone broth that they claim is like homemade. It seems we would be able to take them at their word. It’s much more expensive than making your own though.

      • It really is easy to make. And so totally worth it. I love to cook but never realized what I was missing by buying store-bought broth. Since I’ve been making my own, it’s taken my soups to a new level. In fact, it’s so darn good, sometimes just a cup of the broth makes a great “snack”.

      • Chris, I’ve recently started making bone broth with grass-fed bones. You mention fat as being one of the benefits, but one large bone generates an enormous amount of fat. (I just pulled a 2″ plug of solid fat off the top of my jar of broth).

        So what do you do with all that fat? I couldn’t eat it in a soup. Any way to cook with it?


        • Hi Peg!

          If you’re using beef bones, the fat you have from making the broth is beef tallow, which is great for cooking! I usually just pull it off the broth once it’s solidified, re-melt it on the stove, strain it (if needed; usually it’s already clean enough for me!), and store it in a jar in the fridge. You can use it to cook pretty much anything savory, but I especially like it if I want to “deep-fry” things. It’s not actually deep-frying, but I use a decent amount of fat when I’m making things like hash browns, and I like using the tallow because it’s very stable and it’s cheap!

        • The farm where I buy my meat and eggs from sells “homemade” chicken stock. Just a thought ….check the farmer’s market if you don’t want to make the stock.

      • Gotta hunch this won’t fly for stock, but I usually use Knorr Bouillon Cubes when making soup. Is there any nutritional value for them? Anything detrimental?

        • Sorry, but those are no good and will give you none of the benefits of homemade broth. Here is the ingredient list: INGREDIENTS: Salt, Monosodium Glutamate, Beef Fat, Partially Hydrogenated Cottonseed Oil, Yeast Extract, Caramel Color, Dehydrated Beef Stock, Dehydrated Vegetables (Onion, Carrots, Parsley), Turmeric, Disodium Inosinate and Disodium Guanylate, Spices.

          Hydrogenated fats, msg, fake coloring, tons of sodium and a bunch of other industrial ingredients. I’d ditch this fast. Homemade broth really is easy to make and you can make a large batch and freeze small amounts in freezer bags.

          • I find that home made bone broth such as chicken or beef seem to be very weak in flavor for soups even after adding spices and vegetables. will adding an Organic Bouillion cancel out the benefits of the bone broth or will it still maintain it’s nutritional value as well as adding flavour?

  100. I’m on the Antibiotic Protocol for a serious autoimmune disorder for the past 3 1/2 years. The treatment has helped my condition tremendously and the alternative is deadly, so I am not likely to give it up.

    What do you suggest I do in terms of probiotics? I currently take either one Culturelle daily or 2 PB-8s. Is that enough?

    • I made some suggestions for probiotics in the article. Prescript Assist and saccharomyces boulardii are good choices when you’re taking antibiotics.

      • I have IBS and use Prescript-Assist with great results. Regarding the Prebiotics I use a product called Heather’s Tummy Fiber, which is Acacia Senegal Fiber. I had tried Inulin, metamucil and it made my cramping worse. I now take Acacia Fiber daily with good results. I now only need to take the Prescript Assist three times a week. At least unless I really have to take antibiotics again!

        • Aloe Muciliginous Polysaccharide (AMP) capsules is a highly concentrated form of Aloe Vera and a natural antibiotic. Use that for IBS. It is used for Diverticulitis also. It works.

        • I use Heather’s Acacia senegal (aka Tummy fiber) as a prebiotic as well. I have IBS symptoms and it helps tremendously. Thanks for posting this. I’m wondering what Chris Kresser thinks of Acacia senegal as a prebiotic.

      • you can use AMP instead. see my posts under diverticulitis topic. they will cure the diverticulitis. no need for antibiotics.

      • what would you suggest?

        My wife dealt with many bouts of sinus infections and was given may doses of antibiotics. She then began having serious gut issues. She switched to a pure paleo eating meats, veggies, butter, coconut oil, etc. things got worse and she eventually was diagnosed with ulcerative colitis earlier this year. They wanted to start here on steroids but she decided to go with a GERD diet with bone broth, cooked carrots and broccoli coconut oils and other GERD foods. She has stopped all grains, sugar, hi carb foods. Trying to stick with It’s been 3-4 months and she has improved greatly. Also her achy hands and feet have stopped aching. Her allergies were gone too. She lost weight and overall the colitis symptoms (mucus and runny stools) and began having regular stools and everything seems to be working right. She has always had higher cholesterol thinking it’s due to FH. Like above the 200’s. she is 49 years old 5’2 120 lbs her BP is like 100/60 and pulse is usually in the 60’s. she is in great shape. She recently had here blood work done so we could see if she had the big fluffy partials. We got the results back and we were very shock.
        Here are the results
        Total 398
        LDL-C 290
        HDL-C 104
        TRI 58
        Non-HDL-C 294

        Apo B 198
        LDL-p 3150
        sdLDL-C 65
        SDldl-c 23
        Apo A-1 170
        HDL-P 48.4
        HDL2-C 50
        Apo B:Apo A-1 ratio 1:16
        Lp (a) 22

        Hs-CRP 0.4
        Lp-PLA 303

        All were optimal except
        Her free fatty acids were 1.40

        TSH 1.96
        T4 7.1
        T4 free 1.27
        T3 88

        • I wonder if the coconut oil is raising cholesterol. I hear good things about it but also same bad things regarding cholesterol. Some people think it raises cholesterol. How much does she ingest?

      • i’m wondering if you have a recommended brand(s) for saccharomyces boulardii? my husband started a course of unavoidable antibiotics today and we need to get started on the support for this! thank you for all your great information.

    • Look at VSL#3, expensive but very effective. Once you settle with VSL#3 and you are off antibiotics, Nexabiotic routine is also a good thing.

      Personally, I use VSL#3 DS, Nexabiotic, Probiotic-3 and Prescript Assist. I have Ulcerative Colitis. As stated, I don’t use all of them all the time, VSL#3 to prime and rest for maintenance.

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