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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. 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?

  2. 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.

  3. 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.

  4. 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!

  5. 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.

  6. 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?

  7. 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
    By Sarah C. Corriher
    (Coeliac is sometimes spelt celiac).
    It’s a Holy Spirit revelation thanks to Yeshua- Jesus!!

  8. 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.

  9. 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?

  10. 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

  11. 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!

  12. 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?

  13. 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!

  14. 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.

  15. 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!

  16. 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.


  17. 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

  18. 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,

  19. 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