The High Price of Antibiotic Use: Can Our Guts Ever Fully Recover? | Chris Kresser
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The High Price of Antibiotic Use: Can Our Guts Ever Fully Recover?

by Chris Kresser

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If you need to take antibiotics and are looking for ways to reduce the side effects, please see this article.

Maintaining proper balance of healthy gut flora is a crucial yet widely misunderstood component of human health. While the development of antibiotics has lengthened our lifespans, our excessive and inappropriate use of these drugs may be causing serious long-term consequences we are only now becoming fully aware of.

These consequences not only affect our individual health, but may even be causing permanent changes to the microflora of all people from generation to generation.

Martin Blaser’s recent (2011) article published in Nature highlights the potentially dangerous long-term consequences that arise from the rampant overuse of antibiotics. (1) He argues that changes in our microbiota may even be promoting the transmission of deadly organisms, as one of the important roles of an intact microflora is to resist colonization by pathogenic organisms.

Blaser also points out that not only does the individual use of antibiotics cause permanent changes in the gut flora, but that infants born to women given antibiotics during pregnancy, or the 30% of children delivered via cesarean section, may be starting life with a significantly altered and insufficient level of friendly gut flora. (2) This is a serious concern because lack of diversity in friendly gut bacteria has been shown to contribute to a large number of diseases and complications.

Unfortunately, even a single course of antibiotics can permanently alter the gut flora.

One study found that after a single treatment of intravenous antibiotics, fecal bacteria tests demonstrated a significant change in the variety of bacterial strains, and the development of the pathogen Clostridium difficile. (3) C. difficile colonization in the gut can lead to serious complications such as severe diarrhea and colitis. (4)

Another study demonstrated that a short course of the antibiotic ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on roughly one-third of the bacterial species. (5) This study also found that while much of the diversity eventually recovered, there were still several species that failed to recover after six months, suggesting that even a short course of antibiotics may cause permanent changes to the community of friendly flora in the gut.

Antibiotics are known to cause diarrhea, which may be due to infection by antibiotic resistant pathogens such as salmonella, C. perfringens type A, Staphylococcus aureus, and possibly Candida albicans, as well the various metabolic consequences of reduced concentrations of fecal flora. (6) These results suggests that disturbance of the normal intestinal flora following antibiotic use may be responsible for the overgrowth of dangerous pathogens.

Research also indicates that infants’ gut flora is significantly affected by cesarean delivery, which requires the administration of antibiotics to the mother.

One study demonstrated significant changes in the primary intestinal flora of infants born through cesarean delivery, lasting at least six months. (7) Primary colonization of the newborn’s sterile intestinal tract normally happens during vaginal birth, and it is unknown whether an infant born with inadequate or unbalanced colonization will ever develop normal intestinal flora without intervention. 

While breastfeeding can help restore some of the natural balance to the microflora, only about 44.3% of American women breastfeed (with only 14.8% breastfeeding exclusively) for the full six months that is recommended. (8, 9) Furthermore, breastfeeding alone may not compensate for the changes in flora associated with cesarean sections, suggesting that many infants may be at an even greater disadvantage when it comes to the proper development of a healthy, functional digestive tract. (10)

Research from diverse fields demonstrates the negative effects of gut dysbiosis and inadequate friendly flora on a variety of health outcomes.

For example, resident bacteria of the normal flora are involved in intestinal mucosal inflammation and patients with inflammatory bowel disease (IBD) have higher amounts of bacteria attached to their intestinal mucosa than do healthy people. (11) Patients with Crohn’s disease and ulcerative colitis are found to have reduced concentrations of fecal Lactobacillus and Bifdobacteria, which protect against pathogenic bacteria, increase mineral absorption and induce the production of growth factor in the gut. (12)

An unbalanced microbiota in the gut is also a contributing factor in autoimmunity. (13) Infection with certain microbial pathogens can trigger autoimmune reactions in joints and other organs. (14) The destruction of healthy gut flora can make the mucosal lining more susceptible to leakage, which some researchers believe is a precondition for developing autoimmunity. (15, 16) It is well-established that the balance of gut bacteria plays a key role in the formation of a proper immune response. (17, 18) A lack of healthy gut bacteria is associated with allergies, IBD, and general autoimmune reactions when this immune modulation goes awry.

New research has linked changes in gut bacteria with obesity. One study found that the gut bacteria of obese subjects differs significantly in species type from lean subjects, and that low calorie diets, restricting either fat or carbohydrates, changed the gut flora and increased the abundance of the bacterial strains found more predominantly in the lean subjects. (19) Another study found that transplanting fecal bacteria from lean or obese mice into mice with sterile guts could affect whether these mice gained body fat, even when food intake was controlled. (20) Those mice implanted with fecal bacteria from obese mice gained a significantly larger percentage of body fat than those transplanted with bacteria from lean mice. The authors hypothesized that certain types of gut flora are associated with obesity due to the increased extraction of energy from the diet. I’ve written about this in more detail here.

These studies demonstrate the wide range of potential consequences caused by the improper development or destruction of the intestinal flora.

Though antibiotics may be necessary in certain situations, it’s important to weigh the benefits of using them with the potential risks that may come from the permanent alteration of the gut flora.

If antibiotics must be used (and there are certainly situations where this is the case), special care should be taken to not only restore their gut flora using probiotic foods and supplements, but to eat a diet that supports healthy gut microbiota with plenty of fermentable fibers from starch and the removal of food toxins.

To protect infants’ gut health, especially those infants born through cesarean section, it is crucial to exclusively breastfeed for at least six months, with breastfeeding continuing on-demand throughout the complementary feeding period (up to 2 years of age). I also recommend using a high-quality infant probiotic to help populate your baby’s gut with beneficial flora, as I explain in this article from my natural childbirth series.

Infancy is a critical time where the development of a healthy gut microbiota is essential for the long term health of your child. You can read more about protecting the gut health of your child in The Healthy Baby Code.

In medicine and health, as in all other areas of life, each choice we make comes with consequences. The purpose of this post is not to suggest that antibiotics are “bad” and we should never take them.

As I said in the beginning of the article, antibiotics save lives and have significantly lengthened our lifespans. But that benefit has come with a price, and it’s one that we’re only just beginning to understand the full implications of. My goal here is simply to raise awareness of this price – the harmful and potentially lasting effects of antibiotics – so that you can make a more informed choice.

What are some alternatives to antibiotics?

Mark Sisson wrote a good post listing some alternatives to antibiotics a few months back. In my practice I use a combination of botanical anti-microbials, biofilm distruptors (bacteria often live in extracellular matrices called biofilm, which protect them from our innate immune defenses and any external anti-microbials we might take), and probiotics – as well as micronutrients to support immune function, like vitamin C, iodine and selenium.

While these botanicals do have an impact on the gut flora, it is less pronounced than the effect of broad-spectrum antibiotics. Still, I recommend taking any strong anti-microbials under the supervision of a qualified health care provider.


Join the conversation

  1. Intravenous Vitamin C is a wonderful natural, safe, alternative to antibiotics. Known for years, but suppressed by drug companies and not taught to medical doctors.
    Check your yellow pages for clinics that handle IV C.

    Humans are one of the few animals that don’t produce C in their bodies.

  2. I was prescribed a strong med for C.diff because I was at high risk. Yet, haven’t gotten results back yet to confirm. I’ve been taking the med for a week now & would like to stop. Can I stop if I replace with an abundance of probiotics? I take probiotics 4 hrs. between my doses of antibiotics. Please help!

  3. Do the GAPS Diet by Dr. Natasha Campbell-McBride to heal and seal your gut! Read her book and find a GAPS Practitioner to address your individual issues.

  4. I heard Chris mention on Joe Rogan’s podcast that when he was younger he was treated for amoebic dysentery with multiple rounds of antibiotics after surfing and traveling in Indonesia. He referenced having spent 10 years recovering his gut health and I’m curious what he believes to have been the most effective actions in doing so. I’ve had a virtually identical experience, have essentially recovered, and am curious what I might have done had I understood the potential complications of using antibiotics to treat this type of condition.

  5. Dear Chris most of us have taken antibiotics by now.
    My main question is how to restore the gut flora to max after the damage done?
    Pl respond.

    • Currently medical community has no answer. If you have friends in third world country go there and spend 6 months in place where people poop out and drink water from river. You might rabies as side effects jk. But that the only way out of antibiotics. Going ancestral !!!

  6. been going thru the same bullshit as some of these comments….all started with getting strep throat and a round of antibiotics i now have high level of cortisol [adrenal fatigue] that i have been hit with for going on 4 months just found out 2 weeks ago.. came from i suspected a few things it all STARTED after i developed strep throat and was put on antibiotics the pills didnt do well with me unbelievable diahrrea then i was given the 1 does shot…EVER SINCE THAT DAY i slowly over months got worse and strange symptoms like my hands looked unnormal the palms redness blochyness ….fatigued….after months of this bullcrapE.R visits over 50 times all normal test i eventually went to a endocrinologist high cortisol levels but no pitituary tumor or adrenal tumor…so she said stress……i realized it cant be emotional stress cuz im ok… has to be immune system stress and all came down to something like parasites [only because i made 3 trips out the country eatin tons] or this thing called “candida”….so i did a 10 day parasite cleanse and just started a candida cleanse and removed sugar from my diet when i removed sugar i felt ALOT better but still struggling…think itll take time along damn time…months years idek….i even got b12 pills,magnesium,vitamin c to help my adrenals….doing a 50 billion probotic for stomach…some diotomaceous earth detox for stomach and candida herbal cleanse im on so much shit now idek wut will work wut wont should i make an appt for a digestive doc smh im mad at docs beyond … be honest i know i will be on probotic for a long damn time for sure and a special diet i need help my life sux since this crap

    • Seems like these antibiotic manufactures should be sured for the damages they are causing!
      My life has changed since taking them for ear infections. My shorts list is Mixed Connective Tissue Disease and Thyroid Nodules.

      I see people everywhere are writing about the same life changing experiences after antibiotics. Personally I think doctors must know what is happening, how could they not with all those having problems with grains and Autoimmune disease!

      FED UP!!!

    • That is because the medical industry is run by criminals, like the Rockefellers. They are eugenicists who want to destroy humans’ natural system and put you on a crippling medical system that milks you for every dollar you have, makes you sicker and more dependent, and ultimately kills you. Don’t believe me? Research it. The evidence is everywhere, like air. They mix poison with medicine, like mixing truth with lies. Anyone who refutes this, dismisses it, or trolls this post is a paid shill or useful dupe who is too mentally lazy to research anything.

      • I completely agree with you and congratulate you for such bitter truth remarks.
        it’s time people be pragmatic and look beyond synthetic medication fraught with killing side effects.

    • Shocked to finally see folks are suffering as bad if not worse then I am. Everyday I search for reason to go on. My distrust and hatred of doctors knows no bounds. The pain and suffering I endure everyday has made my life a living hell on earth. I don’t know who to go to, or who to see. I don’t know if this can be fixed. I have been taking Probiotic 10, four tablets a day and it doesn’t seem to do jack. I take soluble fiber which seems to help some. There has to be an answer on what will work. I get so sick of the false advertisements sent to me claiming to heal me. The one that scares me is where they want me to eat fermented cabbage. My intestines is so stripped that common sense tells me that will really cause me great pain. I wish the pain would just go away or I would.

      • please don’t do away with yourself. my fiancé and I both struggle daily. To top it off I have strep like symptoms and a dry painful cough that started back in September! I’ve never had a cough that stayed consistent and never changed. they put me on amoxicillin! I’m terrified. I tested negative for strep but I was still put on that and multiple other things to treat strep and sinus infection… she looked baffled.. but we all know… yet can’t say anything because then they diagnose us Delusional Parasitosis…. I’m praying we all bounce back from this shit

        • Amanda, for dry painful cough try……eating raw whole almond powder couple spoons 3-4 times a day. (Morn-aft-eve-night). I’m hoping you have no sensitivities to almonds. Keep a few white rock crystal sugar in your mouth and suck on its juice slowly soon after eating the almond powder.

      • Try Dr. O’Hirra’s probiotic in the green box. I’ve suffered from diverticulitis and a perforated colon in the past 2 years. After the emergency surgery for the perf colon I started using Dr. O’Hirra’s. It’s the only probiotic I’ve EVER had any results from – ever. With the ailments I had, I received intravenous Cipro & Flagyl for weeks AND have taken that combo via mouth a dozen times. Since giving up gluten & taking Dr. O’Hirra’s, my hair has started to grow back & my digestive tract runs “smoothly” for the first time in my life. For me this probiotic has given me a new lease on life. I order from Amazon and load 4 AM and 4PM if I’m feeling stressed or have taken antibiotics. Happy to say I’ve only had antibiotics once in the past 6 months…as compared to every day of every month for 18 months before I got well. Give it a try – it’s worth the $35 for the chance it helps you!

      • I have really bad intestines close to removal. I have had recurring foot infections for over two years and the doctors just kept pouring antibiotics in me. Severe bleeds. I took GI Heal from Optimal Health Knowledge and I feel so much better. Not all healed only been a month but I can function. I just ordered more of the herbs in GI Heal so I can increase the effects…hopefully. I do not get any money from this just trying to help.

      • I had the same symptoms, tried many different things. Had taken two rounds of antibiotics two months apart. Had belching, stomach pain, bloating, diarrhea. Test were all negative, 3 ER trips. Florastor was my life saver! On my 6th day & my symptoms are nearly gone.

  7. maybe the invention of antibiotics from the first place was sth wrong. unless u dont take vicious antibiotics doses for serious cases u dont get what i mean.alternative medicine was working from the first day of human history why we stopped to use it on everyday basis? i have got a chronic condition that if i dont take antibiotics it may be really dangerous. the thing that most annoys me that dr prescribes easily one that is targeting all. wouldn’t it better to really have very very targeted antibiotics? i would say policies look at general population for evaluating the safety of a drug but when u fall into that minor category of serious side effects that they say they dont see in majority ur life is screwed. u are kinda ignored even mocked by others or drs about how weird ur symptoms are but these things really decrease quality of life and introducing too much stress.

  8. Hello im concerned because of constant tummy problems and needing to use the restroom frequently. Three years ago I had gotten celluitis and mrsa and was prescribed bactrim. It clears and always comes back and since taking the antibiotic im having weight gain tummy problems so on. Is there anything I can do….my doctor says not worry.

    • First add Coconut oil to your diet, 1 TB a day. Probiotics, 50 billion units with 10 strains of bacteria take 1 a day. Vitamin D3 5000 Units a day, Add a Calcium, Magnesium and Zinc Supplement, a good B Complex, Tumeric, Oregano Oil, either liquid or capsule. A really good daily vitamin too!

      • Renee, you are on the right track but you are still missing the the most fundamental element. It is like trying to plant flowers back in a weed patch. COLOSTRUM is like a garden tractor or tiller. It prepares your intestines for the Probotic flowers that you are trying to plant. You may have to take Colostrum, probotics and good fats everyday for the rest of your life but the best diet in the world will not fix antibiotic damage without COLOSTRUM. Most people have to put the probiotics in the form of an enema initially after adding colostrum to my diet. It is basically the same as a fecal transplant but a little bit cleaner.

        • Robert,
          You seem to know a lot. I have been on Amoxicillan for almost 20 yrs straight. I need to talk to someone who gets this stuff… No one in the medical field seems to care at all…

    • I can tell you your stomach health will get much worse if you keep taking the antibiotic. C-diff will hit you next. There are only 3 antibiotics that can be used to treat that. After that is exhausted they have something new they been doing to help introduce healthy bacterial to the gut and that is fecal transplants. If you haven’t heard of that before you will think I am making it up. Google it to verify. It is real.
      God help you. I live in fear of Mercer and Staph infection because I am not able to use antibiotics anymore. Heck I live in fear of any type of infection. I am not sure how much more my gut can take. I am in agony every day.

  9. I am 21 years old and have been suffering from many gut issues as well as anxiety. When I was 20, I had an infection so my doctor prescribed me Amoxicillin and Deoxycline, two of the strongest drugs. I did eat yogurt while I took them in order to reduce the side effects, but they still persisted and 2 weeks after I developed severe anxiety and stomach issues that put me in the hospital. The doctors did all kinds of tests and found nothing so they assumed it was IBS and anxiety-related. Of course when they say it’s IBS, they mean that they have no clue what’s going on. I didn’t have any issues with anxiety or my gut until I took that course of antibiotics. I was living a happy and healthy life, now it’s like I struggle with these gut issues every single day and anxiety and I’m finding it so hard to cope. What angers me the most is that I was told by a nurse that my doctor should have never prescribed me such strong antibiotics for such a common infection, that I should have been given something else. I’m completely sure that those antibiotics triggered an autoimmune reaction and I’m looking forward to having a fecal transplant done in the future; hopefully it works and I can finally return back to my normal life because right now I just feel helpless.

    • transplant feses from a healthy living person or swallow a pill containing feses (poo as you like) that is enteric coated from that person to restore normality

      • Have you had this procedure. I have heard about it a dr. Philadelphia PA is doing this treatment. My daughter and I believe I have this issue. All my daughters (22 year olds) friends have similar issues. We all use same pediatric doctor

    • and amoxycillin is the first line and is among the weakest, Deoxycline is also an inexpensive and essential antibiotic. Most likely your gut microbes died during the course, so you need to restore it.

      • I have done this at home as a last resort because i was suffering so badly and heard such great things. I used my BF as the donor and after the first couple times we got over the idea and it was easy and no big deal. Unfortuantely it didnt help me much and in fact I started having SEVERE fatigue after eating. Most of my issues come from long term use of antibiotics from chronic strep throat as a kid and then a 2 month course from shingles. I have problems eating ANYTHING, i get headaches, brain fog, weakness, and always would get tired after eating but I would pass out for like an hour, after the FMT I will pass out for like 12 hours now! Before you say insulin / diabetes I have checked that already as well every other test under the sun. I have seen a ND, GI, allergist did colonoscopy, endoscopy, checked thyroid, glucose, SIBO, Candida, no one has answers for me. I used to tak eating for granted and now I have to worry every day every time I eat a bite.

        Regarding the fecal transplant, they say you may have better luck trying different donors as maybe you are not compatible. My BF had gotten a stool test prior and is in perfect health but as optimistic I was it did not work for me. It is worth a try its simple once you get over the initial thought of it

        • Also want to mention at sometimes LARGE amounts of probiotics worked for me. Like 900billion a day, but not so much after fecal transplant. It was super expensive anyway I would do it on vacations and stuff. Rifaximin helped some too.

        • You have to take Colostrum in order for the fecal transplant to be effective. If a fecal transplant is not available then probotic enemas will work. BUT YOU HAVE TO TAKE COLOSTRUM.

          • Whats the best source of Colostrum? I was on this like 20 years ago and remember it helping. I dont know why I stopped, probably the cost. Thanks for the info.

  10. I have been on antibiotics for the last 4 years because of the lung infections that I was always getting. 2 years ago I got a lung transplant and they have had to supress my imune system with several anti-rejection drugs. Since May of this year they have now put me on 2 antibiotics and my gut is screwed up to the max. It is not unusual for me to have everything run straight through me days before I can get it under control. I average being put into the hospital about every 3 months for one type of infection or another. I got out 3 days ago from the hospital where I was getting 7 different types of antibiotics. 3 were oral 3 were IV and I was getting through my nebulizer which I take 2 weeks on and 2 weeks off. I eat greek yogurt all of the time and take a probiotics that has 32 different strains and 85 billion cultures. Since I am home I am down to 3 orals a day and 3 times a day I am taking an IV and my nebulizer of antibiotics. The Doctors tell me I need to lose about 20 pounds but I do not seem to be able to make any headway. To be honest it is hard to get active doing things because of my constant bathroom trips.

    I know that they are just doing what they can to keep the infections down and I have a feeling that if I stop them I will not be around long as I no longer have the ability to fight off infections.
    My question is since I am taking all of these drugs to suppress my immune system and because of that I am taking all of these antibiotics to fight off infections. How can I ever get my gut back to where it used to be. Any ideas?

    • As one with more years on antibiotics than most I can try to answer some of the puzzle of the gut question, but you have to be able to do what you need to do and not cheat for a while.

      Bacteria that is destroyed from our gut can be repopulated but without doctor help it takes longer (they have tools that can help, but they don’t want any of us getting better, so we seem to be on our own).

      Kefir – I make my own from fresh raw milk, but it can be made from regular ORGANIC milk as long as it is not massively processed)

      Bone broth from organic or AT LEAST grass fed and NON antibiotic beef – vegans sorry, but this is one of the best ways to combat all KINDS of bad in our diets – going back to bone broth included in our diet is an imperative

      ALL kinds of fermented (ORGANIC ONLY) food, from sauerkraut, to miso, to peppers, any kind of foods from the earth that are fermented will speed the recovery of the intestines and their flora

      Water – must be filtered – water does not keep the intestines “wet” past the small intestine, the foods must keep moving or they DO become dry and a danger – still, drink 8 cups or more pure water a day

      Caffeine in moderation – herbal teas are always going to be a part of my diet, but I do have a TINY bit of caffeine to keep migraines at bay – but it’s white tea and guayusa (much less jittery, in fact none when consumed alone – not much tannins that do contribute to bad health in the white tea

      – DO be aware that caffeine can and does cause constipation along with sleep disturbances

      EXERCISE – and I mean just walking – how do you THINK your gut moves? Without movement your gut can’t move – just a fact of life

      Three months minimum of the bone broth, kefir etc for the cilia to grow back – but the will be small so STILL be careful and add back in foods that aren’t too fibrous CAREFULLY and SLOWLY.

      Here’s hoping this helps anyone looking to improve their gut health AFTER being destroyed by antibiotics.

      My journey isn’t through – I cheat WAY too much :-/ Pizza is my DOWNFALL lol!

      • I just read your reply on the gut. I think my son now has fructose issues from being on antibiotic for 3 years. Would you think your plan would help his issue with fructose?

      • The one thing that you did not mention. COLOSTRUM. You are doing everything right but it still will not work without Colostrum.

      • If you are trying to rebuild your cilia, avoid GLUTEN! You’re taking one step forward and three back with that gluten-filled pizza. Nobody is talking about the increased usage of glyphosate in our diet. Antibiotics are having a direct effect on our gut biome like a cluster bomb whereas glyphosate (active ingredient in Roundup) is an herbicide affecting our gut like mustard gas. The manufacturer has gotten it to be dispensed in commercial wheat and sugar fields. That’s why organic is critical, along with wheat-free. So, when you don’t see organic, suspect contaminated “natural” sugar, wheat, soy, canola oil, or a cocktail of these. You start buying organic and the producers will start shifting away from toxic components in our food, water and air.

    • My narurapath suggested I take VSL3-DS probiotic, Prescription only, for multi dose anti biotic use. It has 950 billion count of various strains. Expensive but worth every penny. The good news is when you are done with the antibiotics you can completely repopulate your gut with good flora and change your future health forever. Get the VSL3-DS!! It’s a game changer.


    • There is fecal transplants that doctors can do to get gut flora back to normal; you can even do it yourself but you have to make sure you have a healthy donor, like a family member for instance.

    • eat shit
      (from a healthy person)

      long answer: get a feses transplantation or swallow a feses pill (enteric coated so the microbes won’t be destroyed by the stomach acid)

  11. 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?

  12. I would be interest to know if there is any studies from extended use of antibiotics with children. I have been eating quite high doses of antibiotics from age 2 to age 15 and while I know very well what the price has been with my health on some areas, I would also like to know how much damage that has done for my gut permanently. And if I have any hope to repair that damage over 20 years later.

    • I am wondering the exact same thing. I have been taking preventively antibiotics from being 1 years old up to 10 years…
      I am suffering from moodswings, anxiety, depression. Been in therapy for years, did a lot of selfhelp. tried to fix my diet. Reading a lot about gut health and nutrition..
      I am almost 29 now and don’t know how to solve my situation.
      Refusing taking any more meds, but unable to cope with these things. I really wanna know if there is any knowledge about this

      • I would recommend an intestinal cleanse and quality probiotics. Kobucha tea is great. I have seen articles discussing the relationship between the lack of healthy gut flora and anxiety and depression.

      • Of course you can heal your gut permanently as our bodies constantly renew their cells. Keep your hopes up and keep researching. I found that taking the advice seriously to drink at least eight glasses of water a day, so easy to think yeah I drink a lot of water. But really look at your water intake and make sure you’re drinking that full eight glasses. Also get some good probiotics eat a lot of good fermented foods

  13. If I disruupt the biofilm in an effort to make the supplements more accessable, doesn’t it disrupt the biofilm of the “good guys” as well as the “bad guys” I need to target

  14. Beta glucans, and in particular yeast beta glucans can work well as a complementary therapy, both strengthening the innate immune system and possibly contributing to improved effectivness against antibiotic resistant strains of bacteria, as some preliminary research is indicating. In a hospital environment you would typically see a reduction of post surgery infections when yeast beta glucans are administrated. By maintaining an optimally functioning immune system one also greatly reduces the risk of contracting an infection in the first place. Innate immune cells have a specific receptor that is triggered by beta glucans of a certain molecular structure and the mechanism of action is very well understood. More information about beta glucans can be found at

  15. In 2005 Ihad acourse of IM injection of antibiotic because of periapical infection(iatrogenic)three months later ,I started to complain of bloating, abdominal cramps and distention.But the most annoying thing is that I had lost the beautiful configuration of my belly, do you have any solution?

  16. Wow Chris. No mention of FMT and how the procedure(s) relates to replenishment? Astonishing, considering you are touted as an expert on topics such as these.

  17. Hi Chris, from past 7 months my health has become miserable due to digestive problem, doctors are not able to find the cause :(. But after reading your article I think problem is because of antibiotics and I am getting a ray of hope that I would get a solution here.
    First will describe my problem and later probable cause.
    Sequence of the Health Problems I am facing from past 7 months:
    Jan and Feb 2014: Started feeling numbness in legs
    March 2014: Started facing stomach bloating, pain of stomach and uneven bowel movements. Mucus and floating objects in stool. Daily I was drinking 500 ml of milk and when I stopped the milk, I almost relived of all digestive problems.
    April 2014: All of a sudden I had Diarrhea and stated having high lethargy, almost I was fainting. I contacted a doctor he suggested me to take light foods (easily digestible) for eg rice items for some while. After taking light foods my health crawled back to normal, but it started all again when I started having Wheat\Eggs
    May 2014: My doctor found that my B12 level is 130 and gave me B12 injections. Also gave me doses of D
    June to Aug 2014: No improvement, the same health condition continued.
    Sep 2014: Little improvement in digestion i.e. not so sever lethargy after having wheat\Eggs
    Doctor suggests for Ceiliac check, Thyroid check, Endoscopy.
    Everything is Normal, No Ceiliac disease, Normal Thyroid and Normal stomach
    Oct 2014: Doctor starts treating for intestinal infection. Prescribes tab Famocid and a fiber powder.
    Bloating considerably decreases but still dark stools and lethargy continues.
    Doctors finding: He is saying its little intestinal sensitivity.

    Probable cause I am guessing:
    In the last year i.e. 2013 I was hospitalized twice and administered the antibiotics through veins. First in March 2013 and second in Nov 2013.

    Chris do you think the problem is due to Antibiotics? pls help me in solving the mystery. I am frustrated of my health problem.

  18. I really found some interesting points through this article, however a question the notion of “permenant changes”. I do believe that it will temporarily disrupt proper gut biosis. Sometimes lasting years or indefinitely if not fixed, however if one is to start using things to replace and re balance the gut this should work contently.

    To a reader like myself who has to take antibiotics for an extended period of time for lyme disease it paints an ugly picture of recovery and complications. I have always been against the use of antibiotics unless deemed absolutely necessary myself. I was using herbs and a natural approach for a while but was getting progressively worse. Antibiotics mixed with my herbs and bio films buster is what finally gave me good progress.

    Obvious I am one of those exception cases where it is needed and not over prescribed. There is still a lot of fear mongering about risks in antibiotic use and stating things like permanent damage to those of us who don’t really have a choice is disheartening.

    • This is my situation exactly. After I complete my years of antibiotics (next month-woo hoo!!), I plan to do all I can to return my gut to optimal health. I’ve considered a fecal transplant as well. I’ll see first where I can get with low carb, fermented food, cultured dairy, bone broth, probiotics & healthy dirt.
      Considering how healthy i feel currently with a gut disrupted daily by antibiotics, I am hopeful!

    • Me too. Lyme. Long-term antibiotics. Three days a week, two weeks on one week off. Might be as long as 15 months!! I am about 4 months in and trying to do everything I can to mitigate the damage as I go. (Pass the bone broth.)

      Thanks for the information. Todd and Eileen, may the force be with you!

  19. Recent blood work indicated babesius and a suppressed level of Lyme. My doctor has prescribed a 4-6 month regimen of three antibiotics- Mephron, Doxy, and Azith. My original reason for having bloodwork was a chronic low platelet count. No symptoms of Lyme . Her reasoning for this approach was to ensure that the antibiotics had time to eliminate any trace of the bad guys. After reading some of these posts, I am increasingly concerned about this course that has been prescribed. Seems like using a sledgehammer to kill an ant. Any thoughts?

    • I contracted Lyme disease in Australia which must have been difficult as officially it does not exist here. I had all of the symptoms from the bulls eye rash at the tick bite site and every pain, sickness and neurology illness documented I recovered after 3 months and got it again then went to doctor prescribed 15 months antibiotics and got sicker and sicker and I did not think that was possible. I only improved after stopping them and taking a 3 strain probiotic specifically to kill candida which had taken over the body. Now I have severe food and chemical intolerances, light headed, lethargy, brain fog and the list goes on. I wouldn’t not take another antibiotic no matter what and would find some other alternative.

      • I am in exactly the same position. I took 3 months of antibiotics for the lyme, I got sicker and sicker. Lost 20 pounds. It had the opposite effect. Now a year later after stopping the antibiotics, I look normal but I can’t tolerate the things I used to, like white rice and popcorn. There’s an allergy, or candida, or something that breaks out inside my mouth now. I used to have such a perfect digestive system, and I trusted the ND and MD’s that antibiotics wouldn’t hurt me. I feel like such a fool. I should’ve listened to my heart when it said, “Trust the herbs – trust the plants.” If you’re reading this and you’re healing from Lyme, please think twice about antibiotics, especially if you’re sensitive. It may be the biggest decision of you life. You can heal from Lyme using herbs – I’m nearly healed using herbs. The Lyme was NEVER as bad as the effect s from the antibiotics. My journey of healing has been 75% focused on recovery from antibiotics, 25% on Lyme. Sigh.

    • This is a good article in that it gets people to think about a holistic approach. Your doctor shouldn’t be prescribing 4-6 months of antibiotics off the bat and without any symptoms (looks like your imune system has done a pretty good job supressing on it’s one). I am just starting month 2 of doxy+clarithromycin for lyme, and only because I had improved symptoms but some still remaining. I also have that my IBS (including diarhea) disappear with the antibiotics and not return. But if someone was having that as a side effect of antibiotic, then I would hope the doc would take them off that antibiotic, as that is a red flag that your gut is being disrupted. Now please note I have also been on nystatin with the antibiotics to keep yeasts in check with the bacteria, and then 200 billion probiotic (strongest kind they market as being a 7 day only plan) at night so it has time over night to colonize. Antibiotics have been a lifesaver for me, but so have these probiotics and antifungal, as it’s important to keep things in as good of a good balance as possible when undergoing any treatment for disease.

      • Hi Pam,

        What is the name of the probiotic that you are on? I have just taken my first dose of Doxy for Lymes and am scared.

        • Hi Marie,
          I was told to rotate probiotics. I took a Jarrow one for a while and now I am on one called 15-35 something like that. I also take a saccharamyces boulardii one (by Jarrow).

          Hope it’s going well.

        • I too just finished three weeks of a terrible antibiotic for a jaw infection as a result of a root canal. My hands, arms and face are now swollen and very itchy. I have been taking a probiotic by Rejuvenation Science, 25 billion containing many more strains than other brands. It has been effective in the past. I ran out so will reorder on Monday. I can’t believe I am back to square one again with my gut health. I am curious to see how quickly this probiotic will make a difference. You might give it a try.

  20. So what if the damage has been done. I was over-prescribed antibiotics in the 80s and 90s and was my infant child. I have asthma, SIBO, and other issues including inflammation and arthritis. My daughter has enamel issues and asthma, and I worry about her. Her pediatrician prescribe antibiotic after antibiotic for ear infections. It was the pharmacist who finally clued me in. What can we do to correct unhealthy guts?

  21. Chris
    Check out the great properties of Kosher unpasteurised traditionally made sauerkraut. Just fermented cabbage in salt – contains probiotics.

    Please Google the following sentence – HOME REMEDIES TO ALLEVIATE COELIAC DISEASE

    Then go to:- Curing Coeliac Disease Using Naturopathic Techniques…/148-curing-ce…
    By Sarah C. Corriher
    (Coeliac is sometimes spelt celiac).
    It’s a Holy Spirit revelation thanks to Yeshua- Jesus!!

  22. I was misdiagnosed with sinus issues and given antibiotics. I haven’t been the same sense. I had abdominal pain and went to the doctor who at least drew blood to check for h pylori. Test came back positive and of course I panicked. I asked the doctor “what now?”. He said “I have to prescribe antibiotics.” I told him “but antibiotics caused all this”, and he said I know but that is the recommended treatment. I finished the antibiotics and took the breath test for h pylori. It came back negative but I still have some abdominal discomfort. I don’t understand all of this. Does anyone have answers? This has been such a scary time for me. I am 40 years old and has never had issues with my stomach. I now have trust issues towards doctors. Please can someone explain.

      • Johnny,

        Your story is similar to mine.

        I took antibiotics for more than years be bcause doctor recommanded. Before that, i took antibiotics for h plyori bactor whatever. Then, me severe allergy started with severe phlegm all the times last 7 or so yrs.

        Before that i had major surgery more than twice due to some accidents.
        I believe antibiotics did something on me. I tried probiotics at least more than probably 6 months. But i dont see it helps. I feel like being drowned by constant phlegms. My blood test taken about 6 or 7 years ago, when this health problem already started, shows that i am allergic to most of testable airborne allergents. I never tested for food alergy.

        • Start researching FMT transplants. They can be performed at home, and have been proven to work miracles on certain disease processes such as C-Diff. There is potentially a Vasy array of other ailments these treatments can cure, as there is hardly any research aside from C-Diff. It should be noted: the FDA only allows FMT in a clinical setting for the treatment of C-Diff, because they couldn’t argue with the clinical data in contrast to the only other standard accepted treatment for C-Diff, that is; Antibiotics. Rest assured, probiotics alone simply will not work in gut replenishment if your entire system was nuked of it’s beneficial bacteria. I unfortunately know this all too well, personally.

  23. Very relevant to what I was searching for here Chris. My friend’s son-in-law insists on giving antibiotics to his son (now aged two years) every time he has a cold. Sometimes Daniel goes 10 days without being able to empty his bowels.

    How can you persuade his father to stop giving antibiotics like this? Reading your article, this cannot be correct what he is doing and what sort of damage is being done?

  24. i took prescription drugs from the age of 7 until the age of 19 on a daily basis did it do damage to my gut flora balance and in what other ways did it impact my health negatively i felt suicidal after throughout my early and mid 20’s could it be because of the long term use of these drugs

  25. Recently I cured strep throat with doTerra oil of oregano. I got a tooth pulled two days ago and declined the amoxicillin and am using oil of oregano instead. Unfortunately while I was gardening I got dirt in my eye and one of my tear ducts got infected. I was prescribed Tobradex eye drops to use. Will topical antibiotics like this effect my gut? Does anyone know any safe natural alternatives for the eye? I am leaning towards taking this perscription, first time I’ve had antibiotics in 20 years. Thanks!

  26. My 70 yr old mom is visiting and I’ve noticed each time she visits she has digestion, bowel problems. She says she feels better when she eats like me (vegan) so I cannot imagine how she must feel other times. She has taken many antibiotics and never treated her gut bacteria. I have taken few antibiotics but take great amounts of various probiotics/immune boosters in anticipation and after. To what sort of medical person can I send her to help her with this issue?

  27. Joe Perez – I’m with you. I googled “how to recover from antibiotic overuse” and was misled to this article (which is a great one for convincing people not to use antibiotics). Even more helpful would have bee a conclusion explaining how to recover. I have a 5 year old daughter who has had so many serious infections that she has been on antibiotics more than 25 times. I am super holistic-minded and have tried everything under the sun but inevitably a cold in my little one turns to a nasty infection (this latest time, pneumonia). I’m trying to understand what I can do to repair the damage done to her system by all of the antibiotics (apart from the obvious: prebiotic and probiotic).

    • Eat a lot of green vegetables, and fresh fruits . Buy a juicer to juice vegetable and fruit if she’s bored of eating them.

      It works every time!

  28. Can I just say how ridiculous and annoying it is that anytime someone types in anything along the lines of HOW TO repair gut flora, HOW TO recover from antibiotics, etc, they are met with an article saying at the top saying that it may not be possible?

    I refuse to believe that.

    Could we please get a more helpful article giving tips and advice, linking to current research regarding how to repopulate gut flora?

    • Joe,
      So you say you refuse to believe that.
      In a sense you are ignorant of the facts, but in another, you have a point.

      There is ZERO chance of replenishing your it floura by the use of Probiotics alone. ZERO.
      Drink as many kombuchas, eat as much Kim-Chi, swallow as many Probiotic pills as you possibly can: you’re doing NOTHING.

      The (potentially) good news is that FMT, that is, Fecal Microbiota Transplants may possibly re populate the colon with some, or all, of this destroyed beneficial bacteria.
      Most simply aren’t willing to embark on such a gnarly undertaking. You essentially are required to obtain a (qualified) donor sample of someone else’s feces who hasn’t taken antibiotics in years( or ever) , who has a completely healthy gut, and perform an enema on yourself with said donor sample. Super gnarly eh? Indeed. But the science is there. When you’re pushed to desperation though, you’ll try anything.

      • While fecal transplants may indeed be helpful, the notion that probiotics will be of “ZERO” help is sheer nonsense.

        Many specific strains have been shown to repopulate and adhere to the gut mucosa.

        Google Scholar is your friend.

        • Actually they don’t. They are transient. The truth is nothing outside of gut specific strains colonize long-term.

          However, with that said; FMT isn’t he cure all. If you look at the studies the donor diversity is always higher than pre-FMT. Even though FMT helps bring diversity back it never surpasses or aligns with donor samples.

  29. I have taken antibiotics many, many times over my life and reading this and other articles has changed the way that I think about antibiotics. From the time I was a child they were always used to stave off infections, now I see how wrong that is. Can anyone link me to some good articles on ways of rebalancing gut flora? I seem to be having trouble finding many good ones.. Any help is appreciated.

    • Joe Perez, did you ever get any answers or find any information on how to restore your gut flora? Thanks.

      • Johnny,

        To a degree. I no longer take antibiotics unless it is absolutely necessary; which it hasn’t been since writing my original post. To restore I’ve been taking Standard Process Guy Flora Complex, Enzycore, and Gastro Fiber, as well as Transformation Gastro. Also probiotics, and apple cider vinegar. The only other thing is I try and exposed self to bacteria here and there. I drink tap water, I walk barefoot outside in my garden, and get dirt on my hands. Things like that. My research has led me to believe that it takes years to recover from antibiotic-caused gut flora imbalances. I have felt results, and am not as prone as I was before. Hope this helps!

  30. Saccharomyces Boulardii is sold by itself by Jarrow…..This is a major contributor to regaining your immune gut flora…..take this along with a very high multi strain probiotic and drink lots of kefir or eat lots of yogurt…you can ferment your own veggies in salt water brine (drink the brine if you can or drink a TBS of apple cider vinegar in water.
    Every meal has got to have probiotic!….actually all day long I fill my body up with them…..rebuild rebuild rebuild! Refuse to us public restroom antibiotic soaps too…bring your own little bottle or use disposable gloves so you don’t have to touch the stuff when you are out. I have seen probiotic lozenge mints and mouth washes that help restore, I have not tried those yet but all I can say is that
    Saccharomyces Boulardii was so worth every penny I spent on it!

    Some of our health issues can be remedied by using a violet ray machine, it oxigenates and stimulates healing the area that is either infected or ailing. Although some instances cannot be detoured ie…a tooth extraction….very important to take antibiotics for that as your bones are exposed to your mouth germs.


  31. Hi Chris,
    I had a deep scaling done on my teeth in Feb. 2011. It was followed up 10 days of amoxacilin and 15 days of cipro in combination with flagil. At end of March I had a horrible sinus infection which was treated with cipro/flagil for 150 days out of the next 8 months before via a CT scan it was discovered that the root of a tooth was up against or the floor of my sinus had been perforated. I didn’t know the need for the use of probiotics when taking antibiotics at that time. At the end of the 8 month period I was hospitalized and diagnosed with diverticular disease. More antibiotics insued but with the use of probiotics after that. I have now been diagnosed with a cyst on my pancreas, enlarged prostate, enflamed gallbladder and sufferd peritonitis when hospitalized again 10 months later. Non of these disorders where present on the CT scans when I was hospitalized. Is it possible that these are associated. I have lost 20 pounds and can’t seem to put it back on no matter what and am unable to return to work because of my depleated condition….Age 64

  32. My son was born in 2005. Although he was born vaginally and I breastfed exclusively for 1 year and on demand for 3.5 years, he began having gut problems at 6 weeks. I was given intravenous antibiotics during my 30 hour labor because I was (am) Beta Strep positive. We went through 6 months of chronic, green to yellow, smelly, metallic stools as many as 18 times per day and me on the Paleo diet before it was cool. The symptoms have steadily gotten better with the intermittent elimination of various things–gluten/wheat, dairy. He has been diagnosed with IBS. Nothing entirely cures him and I’ve always suspected the antibiotics had a negative impact. The kid is pretty sick of randomly expelling mucus out his rear end depending on his diet any given day. As far as I can tell, he reacts negatively to soy and butterfat and, ironically, yogurt. Other dairy is fine in lesser degrees. Pediatricians have been very baffled (or pretend to know the answer). One suggested possible enzyme deficiency–lipase, hence the fatty stools and reaction to butterfat. This of course made me worry about CF. Our family doc is pretty responsive and trained as an naturopath as well as an MD. Any suggestions as to tests or professionals to consult? Thanks in advance.

    • Kirsten if you are concerned that your son may have CF, the sweat test is what you want. It measures the amount of chloride in the sweat. It’s non-invasive and relatively inexpensive. Contact CF centers in your area and they will guide you on how to proceed,

  33. We are walking petri dishes of evolving flora, ok. Everytime you kiss a person and have sexual relations, the flora are being introduced to other peoples certain strains. New studies show even h pylori as transmitted through saliva. What the community doesnt want to talk about is how sexual relations and kissing many people messes w/ that original flora. Yes, antibiotics kill off gut bacteria, but maybe that is a great chance to repopulate with probiotic foods that aid in fermentation which restores the body with healthier strains. Maybe moms gut bacteria wasnt so healthy anyways. Hmmmmmm

  34. My son is 15, he has Cystic Fibrosis (he’s pancreatic sufficient), his doctors want him to take 500 mg azithromycin 3 times a week, they say it helps with inflammation and reduces the incidence of lung exacerbations. They prescribe it to all their patients. Periodically I refrain from giving it to him because I worry about the long term effects of antibiotics. He was hospitalized last September for allergic bronchial pulmonary aspergillosis while in the hospital he was on IV antibiotics for 3 weeks and 60 mg of prednisone. When he was released he remained on prednisone for several months. I decided not to give him the zithromax because I felt that his gut was in need of healing.

    My question is what do you think about the prophylactic use of antibiotics? His doctors say it’s a subclinical dose but I feel it will still damage gut flora thereby compromising his immune system.

  35. Hello, I am newly pregnant (6 weeks) and am in need of some advice ASAP. I know that this comment is late for this blog post, but I am hoping someone will still be able to help me out. I slipped on a box jump during my workout this morning and took a pretty big gash out of my shin. I ended up at the doctor when it wouldn’t stop bleeding and it is apparently pretty close to the bone. It was too big to do stitches and the Dr. (who is not known to be quick to hand out antibiotics) wants me on one, due to the depth and severity of the injury. If I were not pregnant I would definitely NOT take the antibiotic, as my gut instincts are telling me that I should let my innate immunity deal with it. I am not a fan of preventative antibiotics, (or antibiotics in general) but it is not just my health that is at stake. Pregnancy has made me a nervous mama, And the doctor scared me pretty good with talk of things like bone infections and losing my leg! Any advice or comments are welcome, thanks everyone!

    • I would say go with the antibiotics. Sounds like a potentially serious situation and being pregnant makes it even more important that you avoid any serious complications. Just be sure to take a good quality probiotic on the side. Chris recommends Prescript Assist frequently. I would assume that the antibiotics will be fairly short term since they are to prevent rather than treat infection.

  36. I’m definitely going to do fecal transplant! It’s got a definite “ick” factor but the more research I do the more convinced I am that it is a sound, viable treatment for repopulating my gut. Fortunately my three year old is a perfect donor, she was born at home, breastfed for an extended period, no vaccinations, no antibiotics.

  37. Carol
    They put my granddaughter on antibiotics when she was 48 hours old. Massive doses for misdiagnosed meningitis. The idiots didn’t do probiotics at the same time. She is now six months old. After researching about probiotics and trying for three months to get her to give baby probiotics, she finally did. And within days saw a noticeable difference in tummy trouble. Now she gives them to her two or three times a week. So my thoughts are no irreparable harm has been done if you start her on probiotics. Good luck!

  38. My 9 month old daugher came down with a nasty ear infection two days ago. I didn’t know enough to try and use natural treatments first and now she is on amoxacillan. So I have now ruined her gut flora for life? I, of course, will be giving her probiotics now for the rest of her life (until she is an adult), but even that may not be enough? That really makes me feel hopeless and like I have failed my child.

    • Hi Carol. Please, please, please try to resist that worry — and the general mindset of having “failed” your daughter. For a mom (or dad), that kind of thinking is a potentially endless rabbit hole. You made a decision based on the information you had, and the medical advice you received, and wanting to protect your daughter’s health. This is all we can ever do. Medical decisions are rarely as black-and-white as we’d like them to be. Now you have additional information, and you can use it to the best of your ability, with the best intentions (the same thing you did two days ago). My daughter was born via C-section and received antibiotics for the first 48 hours of her life, and then additional antibiotics through my breast milk for about 10 days… there was no question about the necessity of this, but there *are* things I could have done differently had I known more, and I’ve spent a lot of time beating myself up for not doing them. At this point I am trying to accept that I did the best I could at the time, which is all we can ever do. She’s now a healthy, vibrant almost-3-yr-old — no toddler obesity, no allergies or asthma, no eczema, great immunity, smart as a whip. Knock on wood, of course. But it’s important to remember that “increased risk” does NOT mean that every child will have every problem associated with altered gut bacteria — not by a long shot. Also remember that research on the microbiome and health is in its infancy. If you’re prone to worry and guilt, the Internet is not your friend … better to find a knowledgeable practitioner that you trust. Once again…you have *NOT* failed your child … please wipe that thought from your mind.

  39. It should be considered malpractice to prescribe antibiotics without an adjacent anti fungal, clinic strength probiotic. Fortunately research is now discovering a way of reversing dysbiosis permanently, and the cures are “all natural” lol. The most major being HPI or fecal bacterotherapy aka fecal transplant. These are proven to take up PERMANENT colonization within the intestines, and repopulate. Turns out, you don’t need very much either, as the good guys can’t start overpowering the bad guys even in much smaller numbers..with the help of.a decent diet (breads are fine, unless you are sensitive to them
    The major things you need to avoid like the plaugue are excess refined sugars, and caffeine. Yes this means especially, no pop for you.) and the second is fresh human colostrum, or first milk. This contains over 500 beneficial bacteria that can actually repopulate within the gut, and also help to heal leaky gut.

    And fecal transplants are becoming less gross, thanks to a new “Robogut” machine created at the university of guelph, in ontario Canada. For your own amusement look up “RePOOPulate”. They hope to create the “ultimate probiotic”. Interesting stuff really.

  40. Paul,

    Wow. I don’t even know how to respond. I am so very sorry for what you have been through and what you are going through. I finally convinced my daughter to try probiotics, and the difference in the child was almost instantaneous. Within two days, the crying all the time had stopped. I am convinced it was the massive doses of antibiotics. I, like you, have very little trust in doctors. I am of the opinion most have already diagnosed you before you open your mouth…that you are stupid and they are gods. Her pediatrician took the easy way out and blamed it on colic. Through just observation, my daughter and I have decided that it was the antibiotics and baby has some milk and wheat allergies. I live 15 hours away, see the baby every six weeks or so, and figured this out when the pediatrician who is in the same town couldn’t. Enough of my rant. But I am glad you are taking matters into your own hands. The doctors certainly haven’t helped you.

    Thanks for the post and the time it took you to write. Thanks for the advice. It most definitely underscores my belief that we should take antibiotics only when absolutely necessary.

    I will be praying for healing for you. I am so desperately sorry for what you are living with.


  41. I know this is long after the article was originially posted. But I’m hoping to possibly get an answer to a question. My granddaughter was misdiagnosed with meningitis 2 days after birth (they thought she had it, but didn’t). Course of treatment is to pump massive doses of antibiotics through her little body. As it turned out, the culture was negative. But from then until now at four months, she has had severe gas and acid reflux. Could these issues be the result of the loss of healthy bacteria due to the antibiotics?

    • Hi Sandy,

      I’m no doc, but I strongly think so. I’ve been struggling with both severe gas buildup in my intestines and acid reflux since 6th grade (I’m 24 now). I am just coming to the realization that it is because my GP put me on way to many antibiotics since I was a baby until 6th grade, at which point I started getting frequent sore throats (3-4 times/year for a month each time). I still didn’t make the connection at this point, and the doc proceeded to give me more antibiotics every time I went to see him (I’ve been on every antibiotic under the sun, just to name a few: Azithromycin, Bactrim (Sulfamethoxazole & Trimethoprim), Levofloxacin, Moxafloxacin, Amoxicillin, etc.). Now, at 24, my condition has really worsened. I have a whole plethora of other symptoms, including food sensitivities, allergies, debilitating fatigue, incredible pain, all of which are so bad I can’t even work right now. My heart goes out to your granddaughter, and I urge you to explore every option possible of replenishing her gut flora (i.e. good probiotics – which there are a lot in breast milk. You could also get a powdered probiotic to mix in with the breastmilk for an extra boost). Or, find a local farm and buy some raw goat’s milk (If it’s legal in your state). But, the absolute best way to replenish gut bacteria – this may sound a bit gross – is through a Fecal Transplant (or Fecal Bacteriotherapy). It’s a relatively new procedure (most docs don’t perform it here in North America). I am planning to do one myself at home this weekend with the help of my mother. You basically take a donor’s stool sample (in my case my mother), mix it with saline solution, blend it up, and perform an enema. You then hold it in for as long as possible and then release. Many people do it themselves. Here is a link to an explanation on how to do it by Dr. Michael Silverman:

      I know it may sound a bit extreme, but I urge you to consider it. Dr. Silverman’s paper is about C. difficile, but that’s only because that is the main condition people are doing this for as it’s the best understood. The procedure is only approved for C. difficile where I live in Michigan, hence why I have to do it myself. However, the reasoning behind the treatment for my situation and yours is simple. It’s really just a super powerful probiotic. A healthy human’s feces contains countless bacteria and innumerous different strains – making it more effective than any store bought probiotic – that are essential to a healthy gut. At 4 months old, I’m sure you’re correct in your assumption that the antibiotics have wrecked havoc on her developing system. Shame on those docs. Do you know what antibiotic they gave her? And the dosage? I have found a few research papers on specific antibiotics, but there’s certainly a paucity of good information on this topic. We’re just now starting to understand how vital the human gut flora really is since antibiotic over-usage has become rampant in recent years.

      Anyways, if you tackle this head on you will save her years of continued misery! I’ve had a sore throat for the last 3.5 years because my acid reflux is so bad, and I foolishly let these dumb docs put me on PPIs for “treatment” (omeprazole, protonix, & ranitidine). Don’t let them do the same to your granddaughter! I don’t know if they will even recommend those for babies, but if they do, say no. They have messed me up even more. I spend most days completely silent because it hurts so much to talk, and my stomach distends like a balloon as soon as I start eating anything. I’m excited to try this fecal transplant this weekend though, and I may have to do it a few additional times over the next few weeks and months. Sorry to rant but your situation sounds so much like mine, and I am so dissapointed with our medical system because I have struggled for the past few years trying to figure out what is wrong with me. I’ve seen every doctor under the sun (5 ENTs, 2 allergists, 2 gastroenterologists, 2 infectious disease specialists, a pulmonologist, a speech therapist, and 6 GPs – many of them extremely well educated), dealt with so much pure stupidity and disbelief (I even had one doc tell me it was all in my head; I nearly hit him.), only to have come up short and worse off because of their supposed “treatments.” I’ve combed my medical records and every inch of the internet for endless hours, and finally I think I’m on the right track.

      I would give anything to go back in time and stop the docs, my parents, and myself from taking all those antibiotics and PPIs.

      Best of luck to you and your granddaughter. Feel free to reach me if you have any questions.

      Take care,

  42. I don’t know if you’ll see this or if I commented before- but I had IV antibiotics with my son’s labor. Just one bag/dose and close to birth. We developed thrush later. He is allergic to penicillin, which we found out after one dose for a stupid ear infection I knew better than to give him. We breastfed until he weaned due to my third pregnancy at 17mos. He always had weird bowel movements and sensitive skin. After weaning, his sleep worsened, he developed chicken skin and increasingly worsening eczema. He would cry about his belly hurting and melt down over everything. I kept asking his pediatricians if something was wrong and they said it was normal. Went to a pediatric allergist and he tested negative for wheat and dairy allergies. They wanted me to use a steroid cream. At that point I decided to pull gluten and dairy on my own(He was just over 2yrs). He has greatly improved since then and is just over 3 now. Better sleep, no skin issues, rarely stomach issues, better bowels but still weird. I understand it is a hot topic, but I am so thankful that in addition to extended breastfeeding, we chose not to vaccinate him. I don’t believe his system could have handled them. I would like to see more research done on the affects of these IV antibiotics in labor as the children grow. And I wish I could go back and decline that stupid IV.

  43. I’m traveling to India, and have gotten mixed advice on whether or not to take Malarone or an antibiotic as a precautionary measure against Malaria. I really don’t like the idea of taking something, but am not sure if the risk of Malaria outweighs the potential harm. Would love to hear your thoughts.

  44. Hi everyone I’m 27 and had an abcess lanced in my groin due to an ingrowing hair. The cut was very deep and was always getting infected as it was so hard to keep clean being in the position it was. So the brainless doctors kept feeding me strong antibiotic after antibiotic. Finally after almost a year the wound healed however a week after that the most angry blistering rash appeared in my pubic area. I took yet more drugs to clear that however I now suffer from dry skin on my chest and back and have dandruff and a red blotchy face and neck. And just recently I am being attacked by an angry bright red rash in my armpit. I’ve been on the candida diet for four days now and have noticed a slight improvement as my stools were very loose. Can you help me please I feel like I’m slowly dying and all my doctors want to do is give me more antibiotics which I refuse for obvious reasons….

  45. Hi Chris,

    Thanks for your excellent research. We used your Healthy Baby Code and loved it! Our 6 mo. old exclusively breastfed daughter just got a UTI and was given 2 shots of a broad spectrum antibiotic and is now on a 10 day course of amoxicillan. We started her on probiotics the first night of treatment. She is due for her vaccine at 6 mo. and I wanted to see your thoughts on getting vaccinated after the antibiotics have wiped out her gut bacteria. We are doing an alternative vaccine schedule where her vaccines are spread out, so she should be having DTAP on day 13 of 10 days of antibiotics.

    Given this context, would you recommend waiting longer to get her vaccine? Also, is there something specific that you would recommend to help her gut flora recover?

    Many thanks-

  46. My daughter was born via C-section, and both of us received IV antibiotics for a uterine infection I developed during labor. I’ve been concerned about lingering health effects for her but wondered if, in some way, those antibiotics in the first two days of her life were somehow not as damaging than they would have been later in her childhood, since there were no friendly bacteria to wipe out yet. Or is this wishful thinking? She nursed for 2.5 years, so there’s that. I gave her some probiotics when she was a baby, but not consistently. Any point in doing it now, when she’s almost 3.. and if so, what product(s) do you recommend? I’m happy to say that she’s been healthy and has only taken antibiotics once since her birth (for pneumonia)…that’s once more than I’d like, but many kids I know have had multiple courses for ear infections, etc. Thanks for any insight and advice!

  47. So we have this “farm” of friendly bacteria in our gut. Why then do we administer antibiotics orally? Seems we are maximising the damage by nuking the whole farm just to kill a few pests.

    Speaking of farms, if you wish to a acquire a full (very full) range of gut bacteria, take a holiday on a French farm and eat the local cheeses. As Stephen Clarke said in his excellent book A Year in the Merde, the French believe that bacteria have rights too. You may get some tummy upsets, but it will do you good. If you doubt this check out the French life expectancy stats. One of the best in the world.

  48. Question this post states
    “Research also indicates that infants’ gut flora is significantly affected by cesarean delivery, which requires the administration of antibiotics to the mother. One study demonstrated significant changes in the primary intestinal flora of infants born through cesarean delivery, lasting at least six months. (7) Primary colonization of the newborn’s sterile intestinal tract normally happens during vaginal birth, and it is unknown whether an infant born with inadequate or unbalanced colonization will ever develop normal intestinal flora without intervention. ”

    My wife was never given antibiotic before or after she had cesarean section of both of our children. This just sounds very strange to both of us.

  49. Hello Chris,

    Thank you for the article, i find that there is way to little real information about antibiotic related problems on the internet.

    I have taken Flagyl (metronidazole) for 7 days in the end of february this year and ever since i’ve had severe problems. I took the medicin for some parasite that wasn’t really harmful, but the doctor said it doesn’t belong there and Flagyl doesnt have any serious sideeffects. However during the treatment i started to get flushes in my face and dermatitis all over my body. My skin has become better and i’m only left with dermititis in my face now, but this isn’t my biggest problem.

    Since i’ve taken the antibiotics I have a serious depression, have anxiety, have problems sleeping, low libido, urine incontinence and low energy levels. I’ve had a lot of bloodwork done, and they haven’t found any serious disturbances yet. Furthermore i’ve started taking probiotics and am eating a lot of yoghurt. I also read about soil bacteria being good for depression, so i’ve started working in the garden more.

    Do you have any tips so that i can recover from these horrible sideeffects, i’m really getting desperate. Also how do i get the soil bacteria in my stomach, does this go automatically by working in it, or should i wash my hands badly after working in the garden? Heh, i don’t really know how i get the fastest and safest result. Can you help me with this?

  50. Thank you for this article! I am still unhappy that I had an emergency c-section for this very reason (among others). We are planning to have another baby but I have a lot of anxiety about a repeat c-section vs. a VBAC and one of my big reasons for wanting to attempt VBAC is this gut health issue. Now I am wondering, if my baby needed antibiotics for an illness later on, would that kill off all the good bacteria from vaginal birth and nursing anyway?
    Also, I am planning to make coconut milk yogurt from a vegan culture for my milk allergic one year old now that she’s finished taking a round of antibiotics for strep. Is there anything else I could do to help restore her gut health? I am still nursing her and she’s about 80% breastfed and 20% on solid foods. Thanks very much in advance!

  51. Hi Chris. Thanks for the tweet on this great article! In addition to everything you mention some antibiotics have severe side effects. It’s been a little over 2 yrs since I was poisoned by levaquin. It’s been a long road to health and I made never fully recover but thanks to you I’m getting healthier everyday. Keep up the great work.

  52. So I’ve been taking long term antibiotics for the treatment of Lyme disease and have been on daily antibiotics to prevent transmission of the Lyme germ thru pregnancy and while breast feeding. I take daily probiotics and give probiotics to my girls. Additionally I could add more fermented foods to our diet? and encourage my kids to play in the dirt more!
    Beside these things, what else is there to do but pray?

    • Hi there,
      I was also on antiobiotics during pregnancy and breast feeding. How are your children? My kids are always sick with every virus. So stressful, I’m wondering if you have found any remedies for the gut flora? Hope to talk with you!

      • It is so stressful when our family gets sick! What a bummer!
        I’d say my children have been pretty healthy or averagely sick. I gave my older daughter probiotics every day thru about age 2.5 now it’s hit or miss and my 1 year old gets them more hit or miss (poor second child 🙂 ) I take probiotics daily (HMF brand as recomended by my lyme doc) because I am still on antibiotics, nearly 4 years running now. Both the girls eat alot of yogurt and like kombucha when we buy it. They play outside and we have chickens and a garden. I’ve started washing their hands less after playing in the garden and in the yard. Oh and we don’t ever use antibacterial soap in our home.
        My older daughter just started preschool last spring at 3.5 yo and then we’ve seen a lot more sickness. We went totally gluten free this summer and so far this school year we’ve only had 2 mild colds. Much better than last year.
        I am very discouraged to think we are forever ruined by having ever taken antibiotics. So we do our best and try not to let all this new information stress us out!
        Health to your family!

  53. I had a bad experience with the antibiotic CIPRO about 6 years ago. I was given the drug some 3 times or perhaps 4 times in just a couple of months for a respirtory problem. It eventually caused me to have a tremendous heartburn and reaction of rash. The hearburn left me with no good bacteria at all. From that developed a sensitivity to most food products. I had to eat only about three or four food products which I could tolerate and over a year or so add back into my diet the rest of the food chain items. However, I began to develop a clearing of the throat, heavy mucos in my throat and around my bronchial areas which caused breathing problems. Had to cough up and also take clairtin regularly along with Mucenex. Now, I find the food eaten gets slowed down in the upper stomach and produces GERD. Makes more reflux and mucous in the throat. This week I go for a test to determine why the food is digesting slowly in the first stomach area causing the reflux. All of this I think started with the CIPRO deal. I think it damaged my total area and may have damaged my Vegus Nerve! This has been a struggle for me and I hope I can find some answers and some help now that I have finally discovered all of this. Not sure what however.

  54. Hi
    I have been on SCD for four months and have not been very sucessful. For the last four days I have had just ate protein and nothing else but my D has been the worst it ever has and it feels like my strictures are tightened again. I was wondering is this yeast die off or do I need to supplement with Betaine HCL. I was on it before but was afraid it was aggravating my stricture.
    Any advice you have would be greatly appreciated

  55. Please help?. After taking antibiotics for 2 weeks for peptic ulcer. Feel worst than before. Alot of gurgling in my stomach, burning sensation and pain. I have try taking probiotics, enzymes, and change my diet. No good results.

  56. Hi my name is Socorro Im from Mexico so my english istn good, but I need help
    in february my 2 year old son got sick and his flora was damaged and now he can drink mil, because of lactose, I took my son to the pediatrician and he prescribe my son with probiotics, but he’s still having problem with the milk *lactose”, also the pediatrician said the he must avoid the sweet foods or candies
    and that it could take hip a whole year to re establish his flora
    could you help me please?

  57. See “Fighting for autistic children: The endless battles” for an inside look at what happens when non-verbal autistic patients get staph in hospital settings. And why being a warrior mom or dad is critical in protecting these children.

  58. Hi,
    My son was blasted with antibiotics at birth (c-section). I never had a chance to say no. We believe this caused leaky gut for him. He has been covered in SEVERE eczema since he was 3 months old. We just found out he has at least 17 food allergies (neither of us have any allergies). He is now 14 months and I just weaned him from breast-feeding. Because of his limited diet from all the allergies he stopped growing and was put on formula. It’s called Elecare, it’s amino-acid based and has 55% corn syrup solids. I don’t know what to do! He needs nutrition to heal but, the corn syrup is a toxin. We’d like to try the rotation diet but he only eats a handful of foods. He takes probiotics, gets adjusted twice a week and eats lots of raw foods.

    Do you have any suggestions? Thank you for your time.


      • Thank you so much for responding.

        He is allergic to many of the foods and supplements on the GAPS diet (fish and shellfish, all forms of dairy, all meat except chicken, the top 8 allergens, beans, peas, all nuts, banana, avacado… The list goes on) the allergist says to introduce some of these foods but not the top 8. He becomes anaphylactic to those. On the contrary, most holistic doctors say remove all allergens.

        • Krysten,
          My son had all of the same issues as yours, although he ended up with a feeding tube for a year after loosing tremendous amounts of weight around 18 months. He’s almost 4 and doing better, but we have a ways to go in terms of healing his gut. If I had known then what I know now I would have done my best to get him on the GAPS protocol, obviously avoiding allergens right away. We’re on a full GAPS diet and preparing for intro soon. All I can say is to start sooner than later. Now that he’s 4 he’s much more hard headed about eating, or not eating, certain foods. Remember that allergy tests are pretty inconclusive and the only way to really know if he’s truly allergic to something is to heal his gut.

          • Hi Diane,
            Thanks for the insight. My son is now 22 months old and by rast allergy testing, blood tests, and eating the suspected foods we know he is allergic to at least 30 foods. These foods include almost everything on the gaps diet. He takes a good probiotic and eats a healthy diet of organic chicken, brown rice, quinoa, some fruits, and veggies and he’s never looked better. If we stray from the diet or try to introduce new foods (last week we tried grass fed beef) he breaks out and has diarrhea.

            Anyone know how long it takes for one’s gut to recover from antibiotic use? My son takes probiotics but can’t eat any of the fermented foods suggested so I’m assuming his will take longer. I wish I could post a before and after picture to show you what we are dealing with.

            • Have you tried prebiotic supplements? They help the good bacteria to grow and seem to be more effective than probiotics. Look at reviews on Amazon.

  59. My youngest son was given a ton of antibiotics for persistent ear infections btwn 9-18 months old( he breastfed). Then after major vomiting issues at 22 months, an endoscopy determined celiac.
    Could antibiotic overuse in small children create celiac gut? No one else in family has celiac symptoms or labs.

    • Yes, it could predispose him to that. Diseases like Celiac are multifactorial, and have both genetic and environmental causes.

      • Chris,
        I had the same thing happen after antibiotics, Celiac symptoms. Blood tests have been negative but I cannot eat grains long enough before testing.
        Could someone have Celiac even with-out the genes?

  60. Is it theory or proven that probiotic containing foods can help repopulate the gut? Also, Does the probiotic in the food tend to only help with digestion/utilization of similar foods as the item ingested?

    Does the same scorched earth(gut) observation apply in cases where an inject-able antibiotic is used rather than oral? It seems to me since the gut is technically outside the body the affects of an antibiotic would be reduced than an oral antibiotic that would travel through the gut. I suppose where in the digestive system antibiotics are absorbed into our bodies would be good to know. Anyone?

    • Recent evidence suggests that the primary benefit from probiotics may be immune regulation rather than permanent repopulation of the gut flora. However, consuming fermented foods or probiotics on a daily basis does alter the gut microbiota (if not permanently) and the benefits of both are well-documented.

      • Does this mean that those of us forced to endure long-term antibiotic regimens (recalcitrant Rocky Mountain Spotted Fever) can never successfully repopulate our guts?

        On another track, do you think that coffee enemas ruin gut bacteria? Before needing the abx, I occasionally used coffe enema to stimulate my liver. A lovely side effect was that it completely extinguished my horrible cravings for sweets, leading me to believe that my gut had been populated with unhealthy bacteria/fungus. I tripled my use of strong probiotics & thought I was doing okay, but then RMSF returned, again . . .

  61. I have a question about my son, who is now almost a year old. I know looking back now that I had some underlying gut issues while I was pregnant with him (I’m now on the GAPS diet to try to heal), but I unfortunately didn’t really start learning about “real food” and such until after he was born. I tested positive for group B strep while pregnant and thus received antibiotics via IV during labor. We had a fairly standard, uncomplicated, vaginal hospital birth, and he was exclusively breastfed (I’m still breastfeeding). He’s also essentially been on a paleo diet (plus fermented dairy) since we’ve started solids, and I’ve recently been working hard to get him fermented foods and probiotics (I give him kefir grains and small doses of probiotic powder from Custom Probiotics).

    He’s generally been a super healthy kid despite how many mistakes I made during pregnancy and birth–no skin issues (except heat rash), very few sicknesses, very active and energetic. Before solids, he would poop once every few days, but then that increased to once or twice a day on average after solids (all of which I think is normal). However, the one issue he has had is that he spits up a lot. For a while (before starting solids), it was often 10-15 times a day. It has gradually gotten better, but he still sometimes spits up once or twice a day, even though he’s almost a year old. It has never bothered him and he has never spit up while sleeping, and his weight gain has progressed normally. I know some amount of spitting up is normal for babies, but his has seemed excessive. It did seem to improve a bit when I cleaned up my diet and started GAPS, but that might have been my imagination :). Is this something I need to worry about? Do I just need to wait it out and keep it up with the clean diet and probiotics? Or is there something else I should try?

  62. Three years ago I had outpatient foot surgery.
    Four days later I had a visible MRSA/Staph infection.
    I received an IV antibiotic – Cubicin – for two weeks….I was very lucky I was healthy before hand and it worked as fast as it did.
    Though I still went on a tablet antibiotic for the next 6 or 8 weeks.
    So far so good……uh, not really.
    About nine months after that I started to get strange – for me anyway – symptoms.
    Urination problems, prostatitis (with a discharge – yuck), constipation and low grade stomach pains.
    So I went to a Urologist…and guess what ?….he put me on antibiotics.
    It seemed to all get better (95%)….for a while anyway.
    Then it all came back.
    A friend gave me the number to her Chiropractor who deals with health issues with muscle testing.
    I was on & still am on some specific supplements along with a change in diet….not that I ever had weight issues…I haven’t had a beer, yeast bread, cake, etc in over a year now.
    Here I am today…everything is more or less okay…except I can’t put on weight.
    All my blood test come out great.
    I still have some Reflux that I mainly feel in the back of my mouth.
    My Intestinal Flora has probably changed.
    I don’t know what I’d do if I ever really needed an antibiotic again, or worse…what if I needed to get some kind of hospital surgery again ?
    Deal with those issues if they ever come up, I guess.
    In the meantime…keep taking my probiotics as it is a slight battle.
    Thanks for your Blog.

  63. Great article, Chris! Full of reminders of why nature does things a certain way (vaginal birth). Many people don’t think twice about popping antibiotics. Hopefully many new parents will read your article and take it to heart (or should I say gut?). 🙂

  64. Chris,
    Just had a thought and was hoping you could answer a question. I have begun supplementing with Iodine after reading Dr Brownstein’s book. Any thoughts about Iodine potentially killing the good gut bacteria?

  65. I have an upcoming endoscopy/colonscopy but one thing that is going to be tested on the tissue samples is h pylori, for which ill prob have to take antibiotics. If it does come up positive should I just take the prescribed antibiotics for it or take some alternative for it? I would like to fix the h pylori part but I don’t want to mess up anything else by taking some strong antibiotic and messing up my gut flora or more up.

  66. As a Naturopath I have helped many clients who have taken antibiotics. Prevention is always key, if you do have to take antibiotics ensure you take a probiotic and continue for at least 3 months. Colloidal silver is an excellent alternative to antibiotics and the juice from garlic can be used for kids ear infections, there are many alternatives.

    Many people have candida albicans after taking antibiotics, an overabundance of yeast in the body. A strict diet containing no sugar or yeast and supplements will cure this, although it takes 6 months or longer.

    • hi, I was wondering about a kidney infection, is there anything i can take besides Antibiotics? If not ,is there something i should be taking like pro biotic or? Is there a website or book that has the stuff you talk about i would sure love to read it. thanks

    • Sue Ann,
      How do we kill H. Pylori? I gave in and after 3 days wound up in ER with allergic reaction to the antibiotics. Now they want me on Pylora.
      Before all this I had Never taken an antibiotic in my life except for iv antibiotics in hospital after surgery.

  67. Chris,

    Given that the vast majority of people in the developed world have taken antibiotics at some point or another, I hope that you will soon be offering some advice on restoring normal or normal-enough biota (besides a low-calorie diet as referenced in your post). I also hope you will share your thoughts on whether it was the reduced calories, or the change in macronutrient composition that “changed the gut flora and increased the abundance of the bacterial strains found more predominantly in the lean subjects.”

    And thank you for a thoroughly researched post!

  68. Chris – what about the issue of probiotics derived from soil bacteria vs. probiotics derived from milk?

    And I think an earlier comment asked about your views on colloidal silver – I’d be interested in your response on that topic too.

  69. This line caught my eye – “..lack of diversity in friendly gut bacteria has been shown to contribute to a large number of diseases and complications.”

    Could the same apply if one regularly took a single strain of probiotic, eg Culturelle (Lactobacillus GG). Should one diversify when taking probiotics in other words?

  70. Hi Chris, good article!

    What’s your protocol for bug bites? I know it’s a rare occurrence for most people, but when it happened to me last year I wasn’t prepared. The bites I had became red with a streak extending up my arm which looked alarming, so I went to the doctor who prescribed antibiotics…I took them and sure enough it went away in about 2 days. But then I got 2 secondary infections, likely a result of the antibiotics. What do you think?…especially if Lyme disease or Rocky Mountain Spotted Fever are suspected.

  71. Hi Chris, good article!

    What’s your protocol for bug bites? I know it’s a rare occurrence for most people, but when it happened to me last year I wasn’t prepared. The bite I had became red with a streak extending up my arm which looked alarming, so I went to the doctor who prescribed antibiotics…I took them and sure enough it went away in about 2 days. But then I got 2 secondary infections, likely a result of the antibiotics. What do you think?….especially if Lyme or Rocky Mountain Spotted Fever are suspected.

  72. Thank you for the informative article.
    I have a burning question: what are your thoughts on Dr. Ray Peat’s diet suggestions? (like that fructose are ok, lots of dairy etc.)

  73. Chris

    I’m about to have a tooth implant and the dentist has prescribed three doses of azithromycin; one the day before the procedure, one on the day and one the day after.

    Do you have any views on this sort of prophylactic use of antibiotics? The dentist says there is a high risk of infection with this procedure- hence the antibiotics. Maybe I’d have a better chance of withstanding an infection if my gut bacteria weren’t wiped out at the time? I’m not sure why you would start the day before, but guessing that is supposed to deal with any low grade existing infection.

    I’m thinking I might get he script filled but wait and see whether I start to get an infection before I take any.

    On the other hand the procedure is very expensive and I don’t want it to fail because of infection.

    Appreciate any thoughts you might have?

    • Please be careful with dental procedures. Unlike your typical strep or yeast infection, a dental procedure can result in an infection in the bone. I’ve known someone who lost the majority of his teeth and parts of his jaw due to a dental procedure that got infected. It should help that it’s only 3 days and not months.

  74. I haven’t been following your blog too long, so I don’t know if you addressed this but is what you’re saying about changes to drug flora made when using antibiotics hold true for other prescription drugs as well (e.g., Xanax, Ambien). I hadn’t even considered this as a side effect. Thanks.

  75. My mother has struggled with bad stomach ulcers and had an endoscopy which revealed inflammation. She is now a few days into the gastroenterologist-prescribed 2-week course of omeprazole, amoxicilin, and clarithromycin to treat H. Pylori.

    I’m trying to learn more about the safety of this regime. She’s talked to others who suffered from similar symptoms who found success with this prescription. But I don’t know how blunt an instrument this triple course is, e.g. whether it will cause severe gut dysbiosis or not.

    Do you have any thoughts to offer on how to go about recovering from this course of antibiotics? Is there somewhere can I go to learn about this particular regime?

    Would the answer be to simply try and rotate through a few brands of probiotic supplements and regularly eat fermented foods when the 2 weeks is up and then hope for the best?

    Thanks so much for this article and for any ideas you can offer!

    • Michael
      How did your mother make out after the treatment and what did she end up using to help get her back to normal

      I just got off the next stage of the antibiotic treatment using Tetracycline , metronidazole , Lansoprazole and pepto bismol for two weeks and my stomach is a mess

      Any help would be great

      • Jack how is your mother doing? The Dr’s want me on same Protocol. Scared to do it but want the bug dead… It’s realest havoc with my life.

      • I too just got off the same treatment and am still having issues with my stomach 5 months after and am only now starting a daily probiotic regiment and lets see how if it makes improvements , no alcohol , pop , only one coffee a day and proper diet Good Luck

  76. Hi Chris,

    Do you agree with Dr. Campbell-McBride that mothers-to-be with compromised gut flora should apply homemade yogurt daily to breasts and vaginal area prior to natural childbirth?

    Thanks for the great article!

  77. Chris, what do you recommend for biofilm disruption? I’ve read a lot of conflicting information on this. What’s your take on fiber digesting enzymes and lactoferrin for biofilm disruption?

  78. Thank for this informative article Chris. I have been reading your
    posts for a while and enjoy them. Unfortunately my daughter had
    complications at birth and received IV antibiotics in the Nicu, but
    she breast fed for a year and has not had one since, although
    her pediatricians have tried there best!

  79. What if the baby’s mom most likely has altered gut flora, such as women with IBD? Is it still as beneficial to have the baby naturally rather than c-section even if the mom’s flora is most likely not ideal?

  80. Chris – I’m fighting a staph infection right now. Is there anything besides Rx antibiotics that will work on staph (it’s not mrsa).

  81. hi chris –

    what about abx in the tx of SIBO? also, is there an issue with taking bifidus strains when there is no colon present? i’m concerned it might feed the bad bugs…

    • Rifaximin isn’t as broad spectrum as some of the other antibiotics, so may not have as globally harmful an effect on the gut flora. That said, I prefer dietary and natural anti-microbial strategis for treating SIBO.

      • Will you be doing a SIBO blog post soon? PLEASE!! … until then, can you share some of your “dietary and natural anti-microbial strategies” with us?

  82. Excellent article. So I’m a prime example of someone who hasn’t fully recovered from antibiotic use after 4 years, following 3 months of antibiotics to heal an infection in my C-section incision. I have tried Dr. Ohhira’s probiotics, other probiotic brands, Inner Eco kefir, kimchi, sauerkraut, along with a Paleo no grains, no sugar diet. I still get the burning in my stomach and throat daily. After reading Dr. Jaminet’s book, I decided to add “safe starch” to my diet, which I’ve been doing for the last 2 weeks, and I’m hoping for some type of improvement. One of my New Year’s resolutions is not to go to a doctor’s office in 2012. It’ll be a cold day in Hell before I take antibiotics again.

    • If you are taking all that you might have a bigger problem than just probiotics can handle alone – mine needed the extra boost of a gentle boost of organic balsamic vinegar – buffered in a bit of oil – on cabbage – the perfect alkaline cocktail before every meal – I got used to it and when my stomach starts turning sour again I just on the cabbage wagon for weeks at a time – if I find I am bored (I rather don’t usually – but it does happen) my body will “prod” me back to it.

      My fav besides just the balsamic vinegar, a bit of organic spaghetti seasoning sprinkled on top, pink salt with better mineral content and a lot more alkaline, and organic fresh pepper, salsa (Yes, I know pace might be gmo, gee I hope not, shhhhh) and a bit of organic sour cream,raw white sharp cheddar cheese, and viola you have a change of pace taco salad – and I just don’t miss the meat when I can’t afford it 😉 Oh and tomatoes top if off, organic of course!

      • OOPS!

        The balsamic vinegar does NOT go in the faux taco salad – that’s my OTHER favorite but it’s not in the taco version – how about some editing love here lol!

    • Organic balsamic vinegar – base and turns off the burning in a sour stomach.

      Also you need to be checked for bacteria in your stomach that can NOT be handled without a stupid antibiotic.

      If no bacteria – then the probiotics with getting rid of acidic foods and drinks (soads, coffee, non-herbal or organic teas) will help.

      It if persists there is more “wrong” than you know yet.

  83. I every 3 or 4 months i use an antibiotic for my throat, in fact right now i have an infection
    what can you recommend me, please?
    i eat paleo but it is always the same with my throat
    thanks for the article!

    • I used to get strep every 3 months from allergies that caused sinus drainage that caused strep. One day I asked the friendly hippy employee at whole foods in the natural medicine aisle and she recommended Echinacea Goldenseal Propolis. And it actually worked. I have been using 5 years and had only once case of strep it couldn’t prevent. People used to think its was an antibiotic but researched showed it actually an anti-mucosal. I assume it affects you less than anti-biotics.

  84. Hi,

    I feel like this describes my problem, I have develeoped a lot of gut issues after using minocycline for 6 months straight to treat acne (biggest regret of my life). After going paleo, and practicing gut healing protocols, including the one from the recent acne post on this blog, is there any hope for normalcy? At what point do I consider fecal transplants, and how could I go about doing this in the U.S. if I don’t have C Diff. ??

    Thanks in advance for any feedback

      • Yes, you can heal your digestive system but it isn’t cheap.

        Probiotics – huges one – over 10-20 billion units of probiotic are needed to help repopulate the good bacteria.

        Eating less leptins from wheat and other substances is also helpful – even just Organic wheat or spelt will “hurt less” or not at all for those not completely gone to celiac.

        After 40 years of antibiotics I am ill – acquired lupus, sarcoidosis and so much more including sleep apnea from damaged lungs from MISDIAGNOSES and the drugs used when I was under the massive misdiagnosis.

        There are more things to help rebuild your digestive system – the key is to start with a clean bill of health – stomach not bacteria’d with h-pilori – then the healing can begin with better foods, useful teas and probiotics.

          • To kill the H. Pilori, you have to take the antibiotics to kill it – sorry but, been there, done that and know it’s necessary to make SURE it is dead or your guts continue to degrade and you become “me” years later – full of painful sarcoids or lupus tumors when your body’s immune system is all but gone from the abuse medicine and chemicals do to our bodies.

            Find a GOOD doctor or a GOOD naturopath and get rid of the bug FIRST then go full probiotic and exercise.

            Don’t let one round of h. pilori scare you, the drugs are a necessity to get rid of whatever allowed it to proliferate – but be wary of “older” drugs and the “newest” drugs.

            If you are put on antibiotics, it’s time to really be cautious about what you eat “next” and be ready to augment your probiotics with enzymes (presently I have little money do I am using Solaray Super Digestaway 180 count).

            Be healthier by choice.

            • I have been fighting this bacteria for years and have gone through 4 cycles of antibiotic treatments and the final treatment of
              Pepto Bismol — 2 tablets x 4 times per day x 14 days = 112 tablets
              Tetracycline – 500 mg x 4 times per day x 14 days = 112 pills as they are old 250 mg each
              Metronidazole (Flagyl) …. — twice per day (500 mg per dose)
              Prevacid – 30 mg … — twice per day
              finally worked and as of May 2014 I am clear of the H. Pilori

              I took the heavy antibiotic treatment back in March — April 2014 and had large stomach issues for over a month after use and am still having issues with my stomach and am only now starting a probiotic treatment and will update in the next month to let you know but anyone fighting this very stubborn bacteria keep up the fight and remember when taking the antibiotics , read up on when to take and what not to take as I was very strict as to when and what I was taking as some antibiotics need to be taken an hour before or two hours after eating and I took the peto bismol first and waited 5 minutes prior to taking the antibiotics , maybe it helped , not sure but it’s gone !!!!

      • I’ve had pretty positive results with olive leaf extract. Been around for thousands of years. Natural anti-inflamatory,anti-bacterian, anti-fungal and yeast buster. No known side effects.

        • My husband has been taking antibiotics for 7weeks for an infection he had on his foot . He has diabetes 2 he is also taking probiotics but I want him to stop the antibiotics because of the side effects. How are you doing now? How long did you take antibiotics for?

      • Yes there’s actually a lot that you can do! Please check out to look at the GAPS protocol she developed to heal and seal the gut. It’s not that difficult to follow and involves feeding the gut cells what they need to reproduce to form an intact gut lining. Protocol involves consuming bone broths, slow cooked gelatinous meats, home fermented products high in beneficial bacteria and good quality probiotics plus a restriction on foods that feed the bad bacteria in the gut. There’s also a good interview with her on dr mercola’s website maybe you can google it. Plenty of info on GAPS on the web. Hope this helps. You may also wants to test for Blastocystis a nasty gut bug that makes it hard for good bacteria to flourish. I’m testing for it today before I proceed with the protocol. It’s associated with a high % of gut problems. Good luck! I wish you the best.

    • HI. I have found great success with colon hydrotherapy. Have you tried this. My gut was out of balance for so long and I finally reached a point of needing a fix and tried this. It saved my life, I know it.

    • Acne? Tell me it’s not just around your cheekbones!

      If you have localized infections on your face after antiboitic treatment get checked for lupus or sarcoidosis, NOW.

      I am fighting for my life after being drugged by doctors who are about as inept as a bad dog catcher.

    • Dietary fibers- fruit/vegetable fibers. They remain longer in the gut, are an important for several healthy strains of intestinal flora, and also help expel waste material during the digestive process.

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