Marks Daily Apple
Serving up health and fitness insights (daily, of course) with a side of irreverence.
17 Nov

The Problems with Antibiotics: They Kill the Good Guys and Make You Fat

Whenever I think about antibiotics, I stymie my inner Star Wars fan and admit that it’s a good thing the Force isn’t real and Art Ayers is not actually a wizened microbiologist version of Ben Kenobi. Otherwise, he’d be internally wincing every few seconds as another round of antibiotics commences somewhere in the world and a few billion flora cry out in terror and are suddenly silenced, never to be heard from again.

I jest, sort of, but this much is true: every time you take antibiotics, billions of domesticated gut flora die. As I mentioned last week, antibiotics are designed not to target human cells, but the same cannot be said for the commensal bacteria living in our guts. See, most antibiotics don’t discriminate between “good” and “bad” bacteria. They target bacteria. They aren’t us, they are foreign entities, but we wouldn’t be us without them. We need them to function properly. It’s a bit like bringing in an exterminator to kill the bugs infesting your house, and the guy ends up killing your dog and making your cat act funny, along with killing the insects. The job is done, and he technically did what you requested, but now you have to tell your kid that Buddy moved to a farm upstate to go be a sheepdog and figure out how to deal with your cat peeing on the sofa and scratching up your stomach (leaky gut, get it?). Not very fun, and not what you bargained for.

The results of a 2010 study on the lasting effects of antibiotics on one’s gut flora are rather scary. Over a 10 month period, three individuals – humans – each went on two courses of ciprofloxacin, an extremely commonly prescribed antibiotic often used to treat bone and joint infections, respiratory tract infections, gastroenteritis, endocarditis, urinary tract infections, cellulitis, infectious diarrhea, anthrax infection, typhoid fever, and skin infections to name more than a few. In other words, it’s regarded as a trusty all-purpose antibiotic, effective across all species (vets often prescribe cipro). So, what happened to the patients’ gut flora populations after taking cipro?

Three to four days into the treatment schedule, gut diversity was lost and composition was altered. What flora remained became more homogenized, and the various ratios of the more than 400 species of bacteria that live in the gut became lopsided. One week after the conclusion of each treatment, gut flora had recovered, but only slightly. It was a shade of its former self. Diversity improved, but not to original levels. Composition began to normalize, but it was incomplete. Things were stable and the diversity/composition protected from further change, but the state of flora being protected was not the same pre-cipro state.

The authors admit that these are uncharted waters. They don’t know, nor do they pretend to know, the lasting effects of hosting an altered microbiome. They don’t use the words “good” or “bad” to describe bacteria. They just know that it’s altered, and – as much as a ten month trial can tell us – perhaps for good.

I dunno – I have an inkling of an idea that maybe, just maybe, forever altering our gut flora isn’t such a hot idea. I think the researchers would agree, but they can’t say anything without knowing for sure, of course. But my inkling isn’t exactly unfounded. We do have some evidence that altered gut flora are associated with weight gain. We even have evidence that antibiotics cause weight gain. Let’s take a closer look.

Foremost, of course, is the widespread usage of antibiotics to “increase the growth” of livestock. I use quotes because what they’re really doing is making the livestock fat by disrupting the microbiome of their guts. One study even determined that eliminating routine administration of antibiotics to livestock for the purposes of increasing weight gain wouldn’t affect dietary protein availability in developing nations. My guess as to why? Antibiotics are increasing body fat accumulation on these animals, rather than purely inducing sheer hypertrophy of muscle meat – unless you know of any bodybuilders who cycle penicillin and cipro – and the resulting weight gain is coming more from fat than protein.

Other animals offer more avenues of understanding the obesity-promoting effects of altered gut flora. Like, say, mice:

A team of researchers transplanted gut bacteria from obese mice into lean mice. The lean mice enjoyed a 60% increase in body fat and a rapid, 14-day descent into insulin resistance following the gut flora alteration.

In a later study, members of that same team induced obesity in mice through diet. As they fattened, a specific type of Firmicutes bacteria bloomed – it began to overgrow in the gut. Transplanting this Firmicute into lean mice made the lean mice fat. Lean mice who received transplants from lean donors did not get fat.

Oh, and there’s also some cool evidence in humans. Those same researchers who showed that lean mice have different gut flora than fat mice and that transferring fat mice flora to lean mice made the lean mice fat studied whether this was true in humans. It is. Just like the mice, lean human guts contain more flora from the bacterial phylum of Bacteroidetes and less from the Firmicutes phylum, whereas obese human guts contain flora more heavily weighted toward Firmicutes. Furthermore, both mice and humans with “obese” gut flora (high in Firmicutes) derive more energy from food and have an increased ability to “harvest energy.”

Okay. So it seems pretty clear that gut bacteria plays a role in obesity, and there’s strong evidence that it’s a causal role. But the studies up until now have only shown that altering gut bacteria by adding flora from obese animals to the guts of lean animals makes them gain weight. The question, then, becomes whether altering gut flora via antibiotic usage can have similar effects on weight.

One Martin Blaser, an NYU microbiome researcher, believes he has the answer. Citing the 2010 study mentioned earlier and another that he authored himself, he speculates that not only does antibiotic usage permanently change our gut flora, it also promotes obesity. Blaser examined the effect of antibiotics on Helicobacter pylori, a common member of the human gut biome. While there’s evidence that H. pylori increases the risk for ulcers and gastric cancer, making it a popular target for physicians (even in asymptomatic patients) wielding a hammer made of antibiotics, it’s also been living in human guts for at least 58,000 years. You might imagine that casually flouting such an extended co-history together could have some unintended consequences. You’d be right.

Blaser used US veterans who were scheduled for upper GI endoscopies (close examination of the upper gastrointestinal tract). Of the 92 vets, 38 had no H. pylori, 44 tested positive for H. pylori, and 10 were indeterminate. 23 of the H. pylori positive were given antibiotics, and all but two had total eradication of H. pylori. So, what happened to the 21 subjects who were initially replete in H. pylori but who eradicated them through antibiotics?

They gained the most weight. Their BMIs increased by 5%, give or take 2%. The other vets had no weight change.

Leptin levels increased by 20%.

Postprandial ghrelin increased sixfold.

The ghrelin increase is the most interesting effect to me. It does a number of things, the foremost of which is to increase hunger. High levels also increase abdominal fat. So, after taking antibiotics and losing all their H. pylori, patients weren’t as satisfied after meals, they gained more weight, and the weight they gained was likely concentrated in the abdomen. Bad stuff all around. I’ve written about the dangers of belly fat before; it’s not just a matter of LGN.

Man, antibiotics as growth promoters in livestock really make sense when you put it all together. They give you all sorts of awesome stuff:

More efficient conversion of feed into energy. Lower food costs.

Higher ghrelin levels that promote greater accumulation of visceral fat. More marbling.

Now I’m kinda wishing that Art Ayers actually was a Jedi master and he could use Force Debugging to remove specific strains of bacteria from the gut (Force Choke wouldn’t work because most gut flora are anaerobes and thus don’t require oxygen; also, they have no necks).

More problems next week, plus some solutions. Thanks for reading.

You want comments? We got comments:

Imagine you’re George Clooney. Take a moment to admire your grooming and wit. Okay, now imagine someone walks up to you and asks, “What’s your name?” You say, “I’m George Clooney.” Or maybe you say, “I’m the Clooninator!” You don’t say “I’m George of George Clooney Sells Movies Blog” and you certainly don’t say, “I’m Clooney Weight Loss Plan”. So while spam is technically meat, it ain’t anywhere near Primal. Please nickname yourself something your friends would call you.

  1. Antibiotics clearly have a dark side (more star wars there…). To be honest though, I don’t know what I would have done last winter when I got strep throat without them. I was almost completely immobilized and hallucinogenic, and it just got worse for 3 days until I started the antibiotics. Within 2 days I was fine. Finished the 10 day treatment, took a bunch of probiotics (and ate yogurt), and I’ve been fine ever since. Hmmm…..

    Graham wrote on November 17th, 2011
    • Sometimes antibiotics are the only tool for the job. They still do save lives. Over use is the problem. I personally think that a course of probiotics should be prescribed with a course of antibiotics.

      Ingvildr wrote on November 17th, 2011
      • And the probiotic course should probably be much longer (ending a week or more after the antibiotics do) to elbow out the uglies that tend to crowd in in the absence of the good commensals.

        Uncephalized wrote on November 17th, 2011
      • Absolutely – the amount of antibiotics prescribed to patients with viral infections (against which antibiotics are useless) is appalling. Instead of unnecessarily sacrificing healthy gut flora, what if they prescribed probiotics to heal the gut to increase health instead?

        Abel James wrote on November 18th, 2011
        • Someone else mentioned it down thread, but I can’t reply there. I can’t believe how prescription happy dermatologists are! I’ve seen two in the last 10 years, and both were very quick to give me pills.

          I took one for a few years… yes… years… with no results. Tried another from another derm, along with medicated soap, that dried my skin out. I got off of that one much quicker.

          NONE of them asked about my diet. I had expected them to test me for allergies, ask about what I ate. They only spent five seconds looking at my skin before they pulled out the scrip pad.

          Lisa wrote on November 19th, 2011
      • I think that’d probably be a waste of money. Every time you took the antibiotic you’d kill the probiotic you took that day. Wait till the abt course if complete then take the probiotices for a good six weeks on an empty stomach every morning and night. Drink real kefir (not the grocery store syrup with same name). Eat kimchi and sauerkraut,yogurt, etc…

        Lisa wrote on November 18th, 2011
      • I totally agree. I hate when people go about bashing antibiotics and complain but if needed to save their lives, they will happily grab millions and shove them down their throats. It’s a simple matter of using probiotics after using antibiotics. Just encourage persons to do that instead of making antibiotics out to be monsters when they very often save lives on the contrary.

        kassy s wrote on July 6th, 2012
      • In Europe they do that — prescribe probiotics w/ antibiotics I mean.

        CL wrote on July 29th, 2013
    • In your case, and in millions of others, antibiotics have there place.

      But, MOST of the time, maybe 80% or more, they have absolutely not place.

      Accutane, minocycline and tetracycline are all used to try and “cure” acne. It’s all bullsh!#. I know because I had severe acne for 6 years. Going primal gave me clear skin.

      Primal Toad wrote on November 17th, 2011
      • Seriously, derms need to stop prescribing antibiotics to treat acne. Acne is ugly, but it’s not dangerous – no one needs to go as far as taking antibiotics for it.

        Acne was especially uncomfortable for me because of my dermatitis, so it would itch like hell too. Yes, I used to take antibiotics for it – not only did it do diddly squat, but I actually felt my health deteriorating. Nothing helped more than switching to an anti-inflammatory lifestyle :)

        Reiko wrote on November 19th, 2011
        • In extreme cases, acne can be dangerous. When I was about 20 I had severe acne, which I ignored until it got painful from the pressure it transmitted to inflamed regions whenever I opened and closed my mouth, or even moved it a little. I then sought treatment; that involved antibiotics, mostly to head off any secondary opportunistic infections that were aggravating the underlying condition and diverting my body’s natural defences from healing the acne proper. I gather that, if I had not sought treatment, there was a chance that some of the acne could have opened up into facial ulcers that would have had trouble healing from the continual movement of my mouth and from any further secondary opportunistic infections – which would have been genuinely dangerous (think possible sepsis).

          Incidentally, the thinking behind treating viral infections with antibiotics is partly to prevent – head off in advance – secondary opportunistic infections and partly in case there is an unrelated chronic, low level bacterial infection which is tying up the natural defences, i.e. to free those up to fight the virus. One official theory behind giving antibiotics to cattle isn’t to give them bacteria that are directly more fattening, but the idea that their “natural” bacteria are giving them a chronic, low level bacterial infection that shows up as a drain on their energy resources and so cuts down on their weight gain. That would still affect fat rather than protein if they were not burdened very much, as their bodies wouldn’t have to compromise on gaining protein – but that’s what “low level” means.

          P.M.Lawrence wrote on November 21st, 2011
        • You have never had 17 painful and bleeding welts from the infection an adult gets called rosacea. This is NOT ACNE. Calling everything acne in relation to antibiotic use just betrays complete cluelessness on this issue.

          I have a ZERO inflammation lifestyle, and still get dozens of enormous welts an scars without doxycycline. Topicals and diet do not work. The sores bleed and are painful and deep. They are NOT clogged oil glands, they are infections. Preaching that it is something you are doing, just increases the stigma for people who suffer from rosacea….

          Thank god we have antibiotics for this.

          Frederick wrote on October 13th, 2012
      • Going primal certainly is not going to save you from sepsis or severe pneumonia. In many instances they have their place. In fact more than 20 % of the time they have their place.

        kassy s wrote on July 6th, 2012
    • I agree. I got a UTI a month ago and holy cow, so glad the cipro made that pain go away! Living with it was not an option. I only had a 2.5 day course of antibiotics and followed with lots of yogurt, etc when I was done. While I understand the point of articles like this, I worry that the more extreme among us will use it as reason to shun antibiotics completely. Sometimes they are life-saving, literally. They just need to be used judiciously in humans and animals both, for real bacteria-related illnesses.

      Kasi wrote on November 19th, 2011
    • For treating strep throat take a look at the benefits of 2.5pH Kangen water. To learn more go to 2.5pH Kangen water will kill strep without altering the bacterial balance in your gut.

      Steve Putney wrote on November 22nd, 2011
    • In case anyone else comes across this like I did: this post is out of date and its actually been determined that antibiotics can help people LOSE weight too. I have NEVER gained weight on antibiotics and I was on them for years for my acne. When I finally quit taking them my heinous acne came back but I got put on accutane. i decided to take probiotics as a precaution. What do you know? Soon as I started those stupid probiotics (under the direction of stupid internet gurus like this) I gained like 10lbs in a month and continued to gain until I finally realized it was them and quit taking them. Unbelievable, considering that over those three months i watched what I ate really closely (even made a food log) and i was exercising everyday–yet I continued to grow an enormous gut! I can only assume all that “healthy” bacteria was sucking every last calorie out of everything I ate. It works both ways people: just like antibiotics you are altering your gut flora with probiotics and that’s not necessarily a good thing.

      Lila wrote on March 23rd, 2013
  2. Mark,

    This was my exact takeaway message from the Weston A. Price conference this past weekend in Dallas (Specifically the all day talk about the GAPS diet).

    The main idea was to use something like GAPS or the Specific Carbohydrate Diet or maybe even a restrictive version of primal or paleo for a short period of time to let the gut and gut flora heal from all the damage that has been done via antibiotics.

    Tim Huntley wrote on November 17th, 2011
  3. The US FDA released an estimate on the amount of antibiotics given to farm animals in the United States. The grand total is over 29 MILLION pounds in 2009!

    That means FAR more antibiotics are used for farm animals (mostly cattle) than for humans.

    And they wonder why we have antibiotic resistant bacteria…

    I went grassfed about three years ago. I’ll never go back to store bought CAFO.

    Dave, RN wrote on November 17th, 2011
  4. Cipro and the family of quinolones is particularly problematic. A single dose taken by a friend resulted in an inability to walk for several months. Another friend had ruptured achilles tendons. And a friend’s mother had severe crippling effects. I’m thankful for antibiotics in the past when nothing else seemed to kick an illness, but I’m definitely wary of medications in general.

    Rick wrote on November 17th, 2011
    • Cipro has a “black box warning” from the FDA –

      A friend who is a part-time tennis instructor tore a tendon after taking a course of CIPRO. Apparently it affects fit folks more than couch potatoes. I am trying to stay away from antibiotics but if I need to take some I am going to ask for Amoxicillin – an old-school antibiotic.

      HillsideGina wrote on November 17th, 2011
    • Interesting side note: I haven’t needed meds since I changed my eating habits to a paleo/primal style. I even eliminated a former daily medication.

      Rick wrote on November 17th, 2011
  5. If you transplant gut bacteria from lean mice to obese mice do they lose weight?

    Mike wrote on November 17th, 2011
    • That’s what I wanted to know too. Why the hell wouldn’t they do both? They already had the experiment set up!

      Uncephalized wrote on November 17th, 2011
      • Yes, I think that’s in the same study. I’ve definitely read a review of that article somewhere – Hyperlipid, maybe? Check the link, it might be in the abstract.

        Lauren wrote on November 17th, 2011
  6. Great post Mark! I want to preface all of this by saying I’m a PhD level microbiologist and have read all of these papers rather recently just because I’m a true super microbiology nerd. I just have a few comments.

    Commensals are a really hot topic now in microbiology which is good. As microbiologists we’re just starting to spend more time studying bacteria in a more “natural environment”, i.e. not suspended in a mega nutrient rich broth in a totally homogeneous mixture. While studying them that way can be important, I think there’s much more to be gained as it relates to understanding their roles in both human health and disease. My specialty is antibiotic resistance and so on a daily basis I’m looking at the results of overusage of antibiotics not just in people, but in food animals (most people probably wouldn’t voluntarily want to play with bacteria resistant to almost everything, but I think its kinda cool).

    I think the most important distinction here is RESPONSIBLE usage of antibiotics. Getting Strep throat and taking your Cipro, while not the best for your gut flora is going to stop the S. pyogenes from causing your sore throat to get worse and causing some rather nasty secondary illnesses. I think its important to remember that like the authors emphasize, the gut microbiota are a dyamic community and the composition is always changing. That’s influenced by oh so many factors. What happens after those 10 months to a year though? That’s a big black box.

    All in all, I just think people should be responsible with their use. If you’re going to take them, be aware you’re going to change the composition of your gut flora, but I don’t think that should deter anyone from using them if they have a serious infection. I think more work needs to be done to outline which “changes” are good and which are bad. Intrinsically changing your gut flora might not be a bad thing. It just depends on which species are there to occupy a niche.

    Just my two cents. Thanks for posting this.

    Brea wrote on November 17th, 2011
  7. The way this is written, it sounds as if people with ulcers should just live with the pain and stomach upset, because they might — god forbid — gain a few pounds. I’m pretty sure that wasn’t your intent.

    If I were the scientist, I would have extended that H. Pylori study. For example: Let’s take those 21 vets who took antibiotics and gained weight. Now put half on primal diet and keep the other half on SAD. Measure them every week or so. Do the gut flora recover? Does the leptin re-adjust? Do they lose the pounds?

    oxide wrote on November 17th, 2011
    • “Allow me to preface this post series with a wholehearted acknowledgment of the beneficial role antibiotics have played, and continue to play, in fighting infections that might otherwise take limbs or lives. Before formal antibiotics, ancient and traditional cultures employed antibacterial herbs, tinctures, and even moldy bread, but regardless of the various methods’ efficacies, they were largely operating in the dark. They knew what worked, but not why it worked. When we use antibiotics today, we (mostly) understand what they are doing on a micro level, and we aren’t (ideally) just relying on hearsay, anecdote, and experimentation. This is a good thing.”

      Mark Sisson wrote on November 17th, 2011
    • I should have mentioned, too, that eradicating the H. pylori didn’t even improve their stomach pain symptoms:

      “At baseline, the 38 H. pylori-negative and 44 H. pylori-positive subjects did not differ significantly in median pain, non-pain, and satisfaction scores (data not shown). Among the 21 patients from whom H. pylori was eradicated, there were no significant differences between baseline and follow-up pain scores [Median (IQR) 9 (2-23) vs. 6 (2-15); p = 0.86], non-pain scores [13 (12-16) vs. 10 (10-18); p = 0.28], or satisfaction scores [13 (10-23) vs. 19 (12-20); p = 0.29].”

      So it made them gain weight without even solving the problem it was supposed to solve.

      Mark Sisson wrote on November 17th, 2011
      • I’m sorry Mark, I didn’t mean to anger you. I had forgotten about the original series preface.

        Pylori doesn’t cause pain, the resulting ulcer does. If the subjects had pylori and pain from ulcer, then antibiotics would have been effective. If the patients had pylori but the pain was caused by something else, the antibiotics will eradicate the pylori but won’t solve the pain. The doctors should have waited for a definitive ulcer diagnosis before handing out the pills.

        I’m looking forward to the next post in this series. I’ve had antis for everything from pulled wisdom teeth to infected bug bites, and I certainly hope my gut flora are not permanently altered.

        oxide wrote on November 18th, 2011
      • NPR’s On Point just did an episode on bacteria and probiotics and how important they are to our health.

        Great stuff in the episode, including 1) how important gut flora is to babies, 2)how the birth process is intricately involved in our gut flora and 3) h. pylori and how it’s not pure evil, it’s actually a vital component of our gut-flora and overall health, and without it you’re more likely to get fat.

        Here’s a link to the episode:

        Greyson James wrote on July 16th, 2012
      • I had H. Pylori – and suffered terrible heartburn, allergic reactions to wheat and weighed 300 lbs. Constant heart arrhythmiam daily and was red and sweaty. I took PrevPack for 2 weeks and certified that it was clear with an upper GI.

        The next month, ALL of this stopped. I lost 45 lbs immediately.

        Please do not cloud that research with third factor noise and agendas. I suffered unnecessarily for 19 years because of skeptics and noise.

        Frederick wrote on October 12th, 2012
        • Thank you for this comment.

          I have an overwhelming amount of symptoms of h pylori which I didn’t realise until recently. I don’t like to feel like a hypochondriac and waste the taxpayers money in the nhs so I self tested for h pylori. It came out positive so I’m making a doctors appointment.

          From symptoms of reynauds disease, huge bloating stomach for the past ten or so years, really bad gerd (paleo low carb is about the only thing that keeps it under some control), intermittent symptoms of elevated cortisol and adrenal fatigue, I find it really hard to lose weight where I know others won’t.

          I’ve recently read all of these things can be related to h pylori, then tested positive and it’s like a big relief to realise I’m not imagining these symptoms.

          I was then doubting myself after reading this article, I don’t want to put more weight on! But if you had such a positive response to the antibiotic treatment then that’s very reassuring.

          Thank you

          Dave Bird wrote on March 21st, 2016
  8. Good post Mark. So what can we do to restore the diversity? Is a bacteria transplant done by a doctor the only option?

    Arnþór G. wrote on November 17th, 2011
    • Stay tuned. I’ll be wrapping up this series (with solutions) next week.

      Mark Sisson wrote on November 17th, 2011
      • Be sure to cover those fecal transplants. It’s hard to beat a 91% cure rate for c-diff!

        Dave, RN wrote on November 17th, 2011
  9. Does taking pro & prebiotics during and after an antibiotics course preserve/restore gut flora?

    Milla wrote on November 17th, 2011
    • It’s supposed to help. From my experience, though, it’s not a cure-all. A couple of years ago, I was in a car accident, and ended up taking prophylactic antibiotics that were prescribed to prevent infections of my accident wounds. Terrible mistake! I have a degenerative neuromuscular condition (muscular dystrophy), and after 1 week of taking the antibiotics, I had lost about half of my strength. It was a very traumatic debilitation. Since then, I have tried to flood my system with pre- and probiotics, as well as drinking bone broth, but none of it has helped — my weakness resulting from the antibiotic use has remained permanent. I’m considering going on the GAPS or other restrictive and restorative diet, if there is a chance that a more aggressive protocol might help.

      Karen wrote on November 17th, 2011
      • Thank you for your answer, Karen, and I hope you get better! The Primal diet should help, plenty of protein & fat for muscular regeneration! So many people with stories of how it helped them overcome debilating illnesses. Don’t give up the bone broth, and eat marrow! You might also look into creatine/protein supplementation, as well as Co-Q 10 and hyaluronic acid, maybe collagen also? Good luck!

        Milla wrote on November 18th, 2011
        • Thanks, Milla! I do supplement with creatine & other amino acids, sometimes hydrolyzed protein, and take ubiquinol (potent version of Q10) on a daily basis. Thanks for your suggestions.

          Karen wrote on November 20th, 2011
  10. So…. Let’s say that you were ill for a bit and had to be on antibiotics. What’s the best way to normalize your gut flora again?

    I’ve noted after having antibiotics that it takes me between a week and a month and a half to get back to the point where hot curry doesn’t tear up my stomach. I presumed this was due to bacterial death in my gut. However, since it does eventually seem to recover, is it possible that our regular gut flora can do so as well (or can be coerced into doing so)?

    Will Gant wrote on November 17th, 2011
  11. When I was 18 (and before I became health-conscious), I began to get moderate acne and was put on low-dose antibiotics for over a year (which is horrifying to me now)! Not only did they not help AT ALL, but I soon developed really bad allergies for the first time in my life, with allergy tests showing that I had miraculously become allergic to almost every tree, shrub, and weed on the list, as well as multiple foods (corn, soy, peanuts, and lima beans… yeah, shocker).

    The allergist actually asked me if I’d ever tried living somewhere where it was frozen for most of the year! Even though my nose was chronically congested at this point, I refused to go on allergy meds. Instead of accepting that I was merely allergic to these things, I knew there had to be REASON that my body was reacting this way. Well, after some self-education, I determined that my damaged gut flora from all of that time on the antibiotics might be the root cause, so I really put my back into restoring the health of their population. I’m happy to report that at this time, all of my allergy symptoms are GONE! Even when everyone else is stuffed up by oak pollen, I’m breathing clearly… and this is after suffering severe inflammation of my nasal passages for almost 2 years.

    It still makes my stomach drop to wonder what irreversible damage I’ve done to my flora, even if everything seems back to normal.

    Elizabeth wrote on November 17th, 2011
    • Elizabeth, I also was on low-dose antibiotics for over a year as a method to treat my acne.

      To be honest, it completely cleared up my skin… but it also really messed up my digestive system… which makes a lot of sense after reading this article.

      Since going off the meds (about 8 months ago) my acne has returned and I can tell all my non-Primal friends think I’m crazy. But a little acne is a lot less scary to me than all the internal damage this medicine is doing to us!

      Becca wrote on November 17th, 2011
      • Have you noticed a difference in your skin since going primal? I’ve been on birth control now for awhile that has seemed to clear it up… but I went on it before going primal. I’d like to get off of it because, as you said, it’s scary knowing that it’s having all of these other effects on my body. I’m hoping that eating clean and primal will be enough to help keep it off for the most part.

        Elizabeth wrote on November 17th, 2011
        • I have been on antibiotics for my skin on several occasions, including just recently. And I also recently really committed to the Paleo/Primal diet (before I was half a$$ing it) and went off the antibiotics.
          1. The antibiotics didn’t really help my skin.
          2. I found the regimen at and it seems to be working WONDERS, following it very carefully. All topical, sounds crazy if you’ve ever tried benz. peroxide before but … try it. Don’t skimp on moisturizer!
          3. I feel so much better since stopping the meds and smoothing out my diet. Less hungry, less cravings, more energy, sleeping better.
          4. I can’t believe the DERMS just put people on these meds like they are candy as a cure-all for acne. It seems close to a crime.

          Alex wrote on November 17th, 2011
        • OCPs have effects on gut flora VERY similar to antibiotics (I think it was the Primal Parent who wrote about this not too long ago). I’m not sure why.

          Lauren wrote on November 17th, 2011
      • My cream for the Rosacia has helped my son’s girlfriend with her acne a lot. It is a prescription medicine Metrogel 1%. She is better when eats gluten-free, but unfortunately can’t do it consistently.

        Galina L wrote on November 18th, 2011
      • Potato and my skin do not get along.

        Oly wrote on August 13th, 2012
  12. This just means we need to get research out there on the effects of the PB/Paleo diet on gut flora as well as general health, risk of heart disease etc.

    We just need to figure out a way to get the research funded.

    Vivian wrote on November 17th, 2011
  13. Sounds like the in diseased guts the anaerobic food chain is breaking down. Same thing happens happens when they feed cows Monensin (a Na+ decoupling agend), which preferentially inhibits metahnogens.
    Firmicutes (like Clostridia) are typically acetogenic and get a big boost in population when there are fewer methanogens eating up all their H2 & CO2 produced from secondary fermenters. Acetate is a short fat that we can absorb and digest – hence the higher energy yield from fermentable foods.
    Interestingly, Scanlan et al. already published a paper showing something similar in people with IBS, Crohn’s, etc.

    Nick wrote on November 17th, 2011
  14. Hmm, I just remembered the time I had strep throat when I was a kid. I wonder if I actually have gotten oral antibiotics – I always thought I have never had any internal antibiotics and was lucky that way, but now that I think about it – hmm. Thanks for the unspleasant discovery! None of the rest of my siblings have had oral antibiotics and they are all thin, dammit. Well, I am having really good results eating this way, so here’s hoping I can change my gut flora quite thoroughly!

    ladycopper5 wrote on November 17th, 2011
    • I’ve has asthma/allergies since I was 5. I would bet money that I was on who knows what antibiotics early on knowing my mother. And now, over 40 years later, still suffer the consequences although I have improved immensely after dropping 60 pounds and eating basically primal for 4 years (high fat/high protein/no/very low carbs/nothing processed). A month ago I was hospitalized for dehydration following a half marathon (we still don’t know why, it’s a long story) and they found a UTI that they even said was probably brought on by the dehydration and made me take anti-biotics even after I told them I would rather do it naturally (grapefruit juice, anyone?) because they cause weight gain but they wouldn’t listen. No I am taking pro-biotics (which I always did anyway) and hope 3 days hasn’t screwed up all the good I have done. BTW eating this way I am now off prescriptions for allergies (try butterbur, it’s wonderful) and only use my inhaler and generic zyrtec anymore. :)

      Trisha wrote on November 20th, 2011
      • Just an FYI… Grapefruit juice, coffee and other acidic foods and drinks will actually make a UTI worse. Unsweetened cranberry juice can help but you’d have to drink large quantities. An active ingredient in cranberry is d-mannose, a type of sugar that is not absorbed by the body to any significant extent. You can buy d-mannose as a supplement. It will prevent UTIs caused by e-coli but not staph. It works by preventing bacteria from adhering to the walls of the bladder. Drink lots of water and avoid acidic foods.

        BTW, forgive my ignorance but it sounds like the Paleo/Primal diet is another variation on Atkins. Atkins was the trailblazer for the low carb diet, and took criticism for decades because saturated fats were perceived to be unhealthy for the heart. But it turns out it is processed sugars that allow for cholesterol and inflammation levels (that are bad for the heart) to skyrocket. I know Paleo is all the rage, but I think credit is due to Dr. Atkins for carrying the torch years ago.

        Anon wrote on June 16th, 2015
  15. When I was a kid they were handed out like candy. Better safe than sorry, here swallow some more antibiotics!

    Grokitmus Primal wrote on November 17th, 2011
  16. Just a question for someone who would know better than I would: doesn’t coconut oil kill heliobacter? I just find it curious because coconut seems to help keep people or animals that eat it trim. Thanks for any help.

    Larry wrote on November 17th, 2011
  17. So…. is taking a probiotic altering our gut flora and bacteria for perhaps the worse? Perhaps just eating a healthy diet getting lean and letting our guts/ digestive system work it’s own magic or gene expression?

    I started taking a Probiotic that has 13 Billion Organisms….. perhaps not a good idea. my stomach seems to rumble more often not, not sure if related.

    Dan wrote on November 17th, 2011
  18. Looking forward to the solutions! Do you take some probiotic blend, yogurt, kefir, kombucha, sauerkraut… All of the above? What’s the best way to a) test if you can improve the gut environment, and b) improve it.

    Also, is frequent burping and farting caused by bad gut environment, possibly by antibotics? Can you reduce it by fixing the environment?

    I’ve seen a bunch of random observations on the topic, but not a good set of steps for diagnosis and fixing the problem.

    Chris Hynes wrote on November 17th, 2011
  19. Please remember that the reason why antibiotics are used in CAFO’s is not because the antibiotics make them fatter faster.

    Cows stuck in feedlots are fattened on corn and soy feed.

    But Cows are designed to thrive on grass, not grains and legumes.

    Once the cows begin eating corn and soy feed, they start to get fat…and their immune systems no longer work properly. Combine that with crowded conditions and literally wallowing in their own shit, and you get Cows who start to get sick and die before they reach their prime, fattened slaughter weight.

    But mix antibiotics into their feed, and they survive long enough to reach maximum weight just before slaughter.

    Keoni Galt wrote on November 17th, 2011
    • Wow. You just described what’s happening to most people almost perfectly. Except we’re designed to eat meats and veggies. Great ananlogy!

      Kristi wrote on November 17th, 2011
    • Cows on feedlots need antibiotics becuase when fed grains thier e-coli count shoots up VERY dramatically. I used to have the numbers but I just recall it being staggering.
      Grass fed cows don’t need antibiotics because of their natural diet. Grains make the gut e-coli friendly.

      Dave, RN wrote on November 17th, 2011
  20. Looking forward to the upcoming solutions. I’m currently in the midst of a six week course of 24/7 IV Ampicillin, for a deep infection in a broken tibia. I think I’ll take a bit of imbalance over losing my leg – but I’ve never really felt comfortable taking antibiotics in minor cases.

    raney wrote on November 17th, 2011
  21. Last took them for a burn wound that appeared infected … good news is I still have that leg.

    rob wrote on November 17th, 2011
  22. antibiotics are wonderful drugs when used in an appropriate way but I’ve been fed between 8 and 15 of these treatments a year for the last 5 years and it does huge damages to your health used that way… Now I take charge of my health and I know that it was wrong to prescribe me these more than half of the time, it was just in case… who cared then that I would feel like shit and get sick so often… because of another drug that had been prescribed… drugs, drugs, drugs… living primal gets you out of this nonsensical way of pretending to cure… when the only thing done is alleviate the symptoms then alleviate the symptoms from the former treatment and so on

    Nossar wrote on November 17th, 2011
  23. After struggling to lose 100 pounds, I quickly regained it after three courses of antibiotics in one year. Worse, the final antibiotic was one to which I had no previously been exposed and I had a very rare reaction resulting in permanent heart damage.

    What would I have done differently? In each case I was not in pain or immediate danger of death, but I was given a new-fangled antibiotic for the condition. This is done as a matter of course if more than 5% of bacteria causing that illness have been found to be resistant to the old stuff. Demand a culture and sensitivity test! Don’t expose yourself to new chemicals unless it is medically necessary.

    I have read of a case where someone with severe digestive problems went to a developing country and exposed himself to human feces on purpose to regain normal gut microbes (he also wanted a particular paracite for his condition). I wonder if more people are going to start doing this, or is western medicine going to start working on gut normalization protocols? It’s infuriating that the best chance of getting well right now is to literally go eat sh**.

    Spiney wrote on November 17th, 2011
  24. I had a sneaking suspicion this was true when I was put on antibiotics my entire jr yr of high school (recurrent ear/tonsil infections and lazy drs who didn’t want to do surgery), and promptly started gaining weight despite a continued healthy diet and exercise plan once I was off of them…

    Not only did it screw up my digestive tract, but I’d bet money that it’s what triggered my endormetriosis, endometriomas and all the issues I’ve had since… since that year, my health has been nothing short of just f**ked.

    I’m now basically antibiotic resistant, continue to eat probiotics constantly. Though, somehow intuitively, I think it’s never going to be right again.

    Michelle wrote on November 17th, 2011
  25. An interesting note on how antibiotic use–while certainly not paleolithic–might have roots further back in the neolithic than we thought:

    cTo wrote on November 17th, 2011
  26. Makes me feel good about the long term Tobramycin I’m starting in a few weeks.

    David L wrote on November 17th, 2011
  27. Very interesting. I just finished a round of antibiotics (for cellulitis) and I noticed that my stomach was extra wonky. I was never hungry but when I did ate, I had no ‘full’ cues. I ended up gaining 5 pounds.

    Tara wrote on November 17th, 2011
  28. I’m thinking about the possibility of a “poop bank.” Like a blood bank, it would store a resource for administration to humans in need, but instead of blood, the Poop bank would have fecal matter to transplant into people who have had their gut biomes trashed by the antibiotics. Fecal transplants are becoming more accepted for treatment of things like C.diff, so perhaps it’s just a matter of time. I bet a person could auto-transfuse, just like with blood, by collecting and storing a sample before antibiotic intervention, and then having it administered after the antibiotics were done.

    Gives a whole new meaning to “Savings and Loan”…

    Tom wrote on November 17th, 2011
  29. Two years ago I had foot surgery.
    A few days later I had a MRSA/Staph infection.
    I then recieved two weeks of daily Cubicin antbiotic IV’s, followed by two months of antibiotic tablets.
    Last winter I started to get strange symptoms.
    UTI’s Prostatitis, some weight loss.
    I went to a Urologist who prescribed—antibiotics.
    It all got better then worse.
    A friend tipped me off that I probably had a Yeast Infection from all the antibiotics….she was right.
    I went natural this time and still take a half dozen herbal treatments along with various probiotics daily.
    That along with the anti-yeast diet has dropped a few more pounds off of me.
    All I can say is I’m blessed that I was healthy before this all.
    It really takes a physical, emotional and mental toll.
    Had I had any medical issues before hand the outcome could have been dire.
    Thanks for sites like this one.
    Now…to make you laugh…one of the surgical screws used to set the bone has migrated loose and out.
    I can feel it…and it has cut back my running….I use the elliptical now.
    There’s no pain, but I know it’s there.
    And they want me to go back to the same med facility to have it removed.
    I’ll live with it as long as I can. lol

    Larry wrote on November 17th, 2011
  30. When I was younger I took antibiotics for my acne but they made my face so red that I stopped. I’m glad for that now.

    I used to get recurrent tonsillitis for which I was always getting prescribed antibiotics but I’ve worked out that strangely enough ibuprofen makes the tonsillitis remediate just as fast as the antibiotics (and is fabulous for symptomatic relief) if I take it early. I theorize that getting rid of the inflammation is reducing the indentations on my tonsils where the bacteria like to hang out because within 2-3 days I’m usually off the ibuprofen and healthy again.

    SophieE wrote on November 17th, 2011
  31. Hi Mark,

    So if you had H. pylori what would you do? You wouldn’t take antibiotics?

    Thanks for the reply,


    nuno h luz wrote on November 17th, 2011
  32. Mark: I really don’t know what the world would do without you around to do all this awesome research and lay all this stuff out for us so we all can know about it. Never before have I given so much thought to things like gut flora, and life’s just better this way. Susan :-)

    Susan Alexander wrote on November 17th, 2011
  33. Mark,

    Interesting information. I generally try to avoid taking antibiotics when I am sick and just let my body heal itself naturally. It seems like this may not be a terrible approach.


    Alykhan - Fitness Breakout wrote on November 17th, 2011
  34. I’ve heard it said that raw garlic/raw onions given to the same obese mice will return their gut flora to that of lean mice, and they lose weight. Is that the case, or just wishful thinking?

    Mari wrote on November 17th, 2011
  35. All meds have secondary effects on the body.
    It depends on the person how they will manifest.
    You might need here and there some pills in case of emergency, but over the long haul, you can enjoy a healthy lifestyle through proper nutrition and great fitness,

    Paul Alexander wrote on November 17th, 2011
  36. Wow! I find the ghrelin increase the most interesting as well. It all makes sense. People with bad nutrition tend to get sick more often, resulting in antibiotic use. Through the combo of poor nutrition and antibiotics, no wonder why we Americans have huge guts. Or should I say…marbling.

    Erik wrote on November 17th, 2011
    • People are even more obsessed with antibiotics here in the UK. I have a friend who takes them for every single little ouch. He also gets sick if someone sneezes within a mile radius…
      And the ‘marbling’ thing made me LOL – thats genius 😀

      Milla wrote on November 18th, 2011
  37. Mark,

    I’ll be curious to hear your solutions post because I’ve been off/on antibiotics for literally years — on it for as long as 10 months at a time (skin issues).

    I hate it, yes. I realize it’s bad. Now I’m on a low-dose antibiotics that supposedly is only anti-inflammatory, NOT anti-microbial in nature. Your thoughts on this? (I know it’s not ideal, but do I at least have a shot at restoring my flora if there’s no antimicrobial activity?)

    Thanks for your research and blog,

    Alana wrote on November 17th, 2011
  38. My husband had spontaneous rupture of a bicep while on Levaquin. And Cipro (and other fluoride meds) are being heavily implicated in the development of fibromyalgia. I just had a cold (virus) go bacterial (green and yellow mucus) and cleared up the bacteria in less than 24 hours using chopped raw garlic on the bottom of my feet (no garlic breath :) – cover with plastic wrap, socks, another layer of plastic wrap, and another pair of socks to keep the garlic from breaking through and stinking up everything – and be sure to put out the trash after you remove it and wash up in the morning – may need to repeat at least once).

    Kathryn wrote on November 17th, 2011
    • wow. I’m with you on the garlic, its helped me through plenty, but I just stick to concentrated garlic capsules from the health store :-)

      Milla wrote on November 18th, 2011

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