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


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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)

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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.

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Join the conversation

  1. 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.

  2. 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.

  3. 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.)

  4. 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.

  5. 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.

  6. 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

  7. 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!

  8. 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?

  9. 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!

  10. 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?

    • It’s a good question. I doubt it’s ever been studied, but I think a vaginal birth would still be preferable.

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

  12. 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?

  13. 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.

  14. 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.

  15. hi Chris-

    any of your thoughts on COLLOIDAL SILVER would be appreciated…

    (you remind me of a young ray peat!)

  16. 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

    • I am also having the same problem. Is there ANYTHING that can help to heal my gut after antibiotics?

      • 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 http://www.dr-natasha.com 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.