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. As a dentist I deal with infections all the time. 300 people a year die of tooth infections in the USA. I agree that many doctors overprescribe antibiotics. Personally I have to see systemic signs of infection before prescribing antibiotics. I always recommend probiotics along with any antibiotic prescription. Looking forward to Mark’d solutions post. Hopefully I can improve my recommendations!

    PaleoDentist wrote on November 17th, 2011
  2. now concerned! I have been on long term, low-dose Doxycycline for Rosacea/acne for about 2 years.
    The antibiotics cleared up my skin a treat, but I have also radically altered my diet since starting them. And co-incidently I have been thinking about giving them up.
    I now am ‘almost’ primal (NO wheat/grains but still eat dairy) and before I changed my diet I was wheat/grains biggest fan!
    And the only thing holding me back from stopping them is my skin flaring up again.
    Oh, what to do??

    Rebecca wrote on November 17th, 2011
    • Dairy can be a huge contributing factor to skin issues. If I have a drink of milk I’m sure to have a few new zits pop up the next day. No dairy = flawless skin for me :) Might be worth a try cutting it out and cutting out the antibiotics if acne is the only reason you take them!

      Jessica wrote on November 17th, 2011
      • Switching from commercial to local-market dairy helped me. I tolerate dairy quite well, grew up on a farm with goats and cows, but commercial dairy – except well-aged cheese – isn’t very good. I buy local, unpasteurised, and it doesn’t give me a single problem.

        Milla wrote on November 18th, 2011
    • You could try eliminating dairy for a while to see, but it is easier said than done…try switching, at least, to fermented dairy, heavy cream & butter and cheese, preferably raw/unpasteurised.

      As for the antibiotics, rather than going cold-turkey, try missing a dose, and see how you do. Then miss another one. Get off slowly, and up your anti-inflammatory food intake (oily fish, berries, etc). And try calendula. Its a very potent anti inflammatory. I don’t have rosacea, but my skin used to be very problematic and sensitive and calendula compresses worked very well. Also try burdock/nettle/dandelion teas, a few cups, well-steeped, a day. Sorts out my flare-ups though you’ll find yourself in the toilet all day – nettle is rather diuretic!!!

      Milla wrote on November 18th, 2011
    • if it is 20 mg doxicylcine 2/day it is the same as Periostat (20mg bid) used in dentistry to treat periodontal (gum) disease. it is a submicrobial dose and will not kill bacteria and therefore will not cause bacterial resistance. it is used for its side effect as an anticollagenase to turn of MMP’s.

      PaleoDentist wrote on November 18th, 2011
      • Thanks Pale0 Dentist,
        It is in fact 50mg/day. Is that still ok?

        Rebecca wrote on November 18th, 2011
  3. I had to take Cipro when I was away trekking in Africa due to very bad diarrhoea a few weeks ago. I was extremely weak in a very remote area and I took what the doctor gave me. I knew the damage I was doing to my gut so I stopped after 3 days and I’ve been knocking back raw milk kefir every day since to try and boost my gut back up again but I’m very interested in any other solutions.

    David wrote on November 18th, 2011
  4. I was always the tough guy and gut most anything out. Including walking pneumonia. Funny thing now is I am not so tough. It devastated my lungs, I can’t run 100 yards now. When you need antibiotics take them.

    Having said that I think in the future they will find interesting interactions between bacteria and auto-immune disease. Could certain chronic disease be cured with certain bacteria?

    This is not a new idea. Phage Therapy has been around since the 1920’s and is gaining renewed interest in the light of antibiotic resistant strains of bacteria. You may wet your appetite for phage therapy starting with wiki.

    Greg wrote on November 18th, 2011
  5. This is depressing. I was given round after round of antibiotics as a small child until they decided what I actually had was asthma. I’m looking forward to the solutions.

    rabbit_trail wrote on November 18th, 2011
  6. This scares me.
    I unfortunatly have a skin condition and I have to take antibiotics daily to keep it in check. There are some problems that going primal won’t fix. Sigh.

    Moonlightmyth wrote on November 18th, 2011
    • With you on this one… take or not to take..that is the question!

      Rebecca wrote on November 18th, 2011
  7. I have been doing ‘all the right stuff’ for a few years….but this past year I was hit with sudden joint pain/fatigue (while continuing with exercise & avoiding grains), next comes anti-inflammatory meds…then stronger pain meds- while waiting for a slew of Doctors to rule out Lupus, arthritis….finally an Infectous Disease Doc has given me my second course of doxycycline- wow- start dropping pain meds and feeling like my old self! So as I am being treated for the bacteria left by a TICK 3 years ago….and praying that this will put an end to it….what I’m reading here is worrisome….after doing my part to be a healthy person- I need antibiotics, lots of it!!
    Though I hate it and cringe with each dose- I cannot deny that this is my only proven chance at recover- really.
    So damned if I do…damned if I don’t ?

    Gracey wrote on November 18th, 2011
  8. I took Cipro for 3 days for a UTI and woke up screaming at night with massive shooting-pain headaches. I talked to a researcher who said one of the side effects of Cipro can be permanent brain damage. In fact his daughter is in her 30’s and had that side effect. She will never be able to live on her own. Thank God for the warning pain–Cipro’s on my allergy list.

    About the acne cures–I’m an esthetician who deals with it everyday. Many of my customers are on antibiotics from dermatologists and they don’t work consistently. But if you read the derm textbooks, they suggest antibiotics as the standard of care.

    Benzoyl peroxide, while effective and cheap, is a potential carcinogen. EPA changed in classification in the 1990s with no fanfare. But if you work in a manufacturing plant with it, you must use a respirator. Not a good idea to use it long term.

    Check out Their products use cinnamon, zinc, green tea, clay and more natural products. I’ve had good results with their products.

    Medbh wrote on November 18th, 2011
  9. I was recently amazed to hear a doctor tell my friend after surgery, that because she was taking antibiotics that she would need to be conscious of rebuilding the beneficial bacteria in her gut. He suggested not only yogurt, but probiotic supplements and true fermented items like kombucha and real sauerkraut. Go doc!

    serrorserror wrote on November 18th, 2011
  10. I had two rounds of Cipro, two winters ago (long story, but it was preventative usage). Didn’t notice a thing. No eating or digestion or weight changes at all. Maybe the way you eat determines the flora population that re-grows?

    Moshen wrote on November 18th, 2011
  11. Do you know if Doxycycline will have the same negative effects as the antibiotic tested? The reason I asked is I am about to be deploying to Afghanistan and I was just issued a bottle of 400 Doxycycline and we are to take one every day for the entire year, which I can imagine according to this story will be quite detrimental to my weight loss/keeping it off.

    PFC. Lopez wrote on November 18th, 2011
  12. Too lazy to read through the comments to see if anyone’s said this yet, but not all antibiotics harm every bacteria in your body.

    For example: the antibiotic prescribed for UTI is fairly specific, and doesn’t harm your gut flora (or so my doctor tells me).

    Of course, even the specific antibiotics have side effects, so there’s still good reason to cringe when your doctor prescribes you an antibiotic regimen. I don’t know about you, but I’m generally not in the mood for vomiting, fever, and stomach bleeding.

    I only take antibiotics if I really think I need to. I’ve gotten two UTIs in the past, and I’ve gotten rid of them both without antibiotics. They’re still pretty terrible, but they’re not evil. You can keep them at bay with enough vitamin C (or cranberry juice). If you do get one, you can get rid of it in less than a week by drinking enough water and consuming tons of vitamin C 😉

    Reiko wrote on November 19th, 2011
  13. How can you reinstate the ‘good’ bugs? Last year I had a major ear infection with 100% hearing loss – and they were worried I would have mastitis leaking back into the brain – so antibiotics were essential.
    But 2 weeks of augmentin (and nexium) wrecked havoc with a coeliac gut, and seriously reduced the amount of HCl I was making.
    The HCl levels are now OK, but I can’t loose the excess weight I gained. I reckon it’s ‘the bugs’. I use probiotics all the time, and have lots of organic yoghurt, but still not good enough.

    Jenny W wrote on November 19th, 2011
  14. two words: fecal transplant.

    FayeP wrote on November 20th, 2011
  15. 3 years ago I had a near death experience. I was given a course of Augmentin which was followed by a horrible antibiotic induced colitis. So sick I though I was going to die. Didn’t go to the emergency room only because I could not get out of bed to get there.

    A week later I was strong enough to go back to the doctor, and they then gave me a new course of cipro. The horrible colitis subsided, but I was left with a giant rock in my gut. I did a 3 day fast/salt water flush and felt a million times better. I was SO careful of what went into my body after that. I adopted the PBP way of eating, quit everything else cold turkey. I was taking a probiotic for about a year after the incident. My GI problems came an went in spells, I lost my appendix 2 years after the incident (RIP little buddy).

    Since the appendectomy, things took a turn for the worse. I was in school at the time and couldn’t afford high quality probiotics. For the year following, I had not experienced a solid stool. Frequently had blood and mucus pass. It was horrible. I always needed to be near a bathroom. As a grown woman, I pooped myself in public on two different occasions. It got REALLY bad a couple months ago (blood, mucus and diarrhea all day every day). I finally went to see a doctor (I’m uninsured).

    Of course the Dr. wanted to do a colonoscopy ($5000-7000 procedure). They did all sorts of tests and stool cultures, decided I probably had ulcerative colitis. Wanted to put me on Rx where the side effects could make me violently ill. I said no thanks.

    I got back on a super high quality probiotic, drank 16oz of kombucha each day, and it only took 2 weeks to have a normal stool again. I can not tell you how liberating it was.

    3 years of abnormal GI symptoms, a hellish last year… Probiotics may have just saved my life.

    antibiotics almost killed me wrote on November 20th, 2011
  16. I had an infection in my “bad” knee last year, which made my knee swell up like a football. Needless to say the pain was unbearable. I was immediately hospitalized, had a tube placed in my knee to drain it, and, of course, I was on IV antibiotics. No weight-bearing on that leg and no movement of the knee was allowed for 1 month. THEN I had to take antibiotics orally for 1 year. I didn’t want to, but the Doc said that the infection would return if I didn’t. I didn’t want that infection ever again, so I was a good patient. Now I suffer from constipation and weight gain that is hard to lose. Boohoo!!!

    Michele Shimizu wrote on November 21st, 2011
  17. I haven’t had to take antibiotics in a number of years….. but every single time I did take them my gut and the rest of my body would explode with yeast. Blech! The probiotics sound like a good idea.

    Mary wrote on November 21st, 2011
  18. First post here. I’m 44 and I weigh 115 lbs after giving birth to 5 kids. Yay primal!
    I see all these people who were prescribed antibiotics for acne. Fortunately/unfortunately that was never an option for me. I cannot take antibiotics. I have had a bad reaction to every single one used so far (my medic-alert bracelet says,”see medical records”) the list is so long. Basically first use- rash, second use hives and breathing problems (emergency room time).
    Any way, back to my point, I had severe acne well into my 30’s. My dermatologist stymied by her inability to use standard treatments on me, suggested avoiding all products with sodium laurel sulfate–which is in most shampoos and body washes. Within a week my acne cleared up and never returned. Turns out, the SLS was irritating my skin causing it to produce too much oil and the overabundance of oil was causing the acne. I wash my hair with just conditioner. You need to use a lot but it works just fine.

    Anne wrote on November 21st, 2011
  19. Mark, Just curious if this issue goes back to my earlier email to you from my China experience. Re: Their pasta laden diet and mostly thin bodies?

    I am not sure if the beef they eat is free of antibiotics (as well as hormones)but that could be a possibility.

    Skip Cook wrote on November 22nd, 2011
  20. Mark, perhaps you can answer this in your next post…

    Regarding the lower Bacteroidetes/higher Firmicutes in obese individuals, I was surprised to learn than many of the probiotics we tend to look for are actually firmicutes, including the bacillus and lactobacillus groups present in yogurt, kefir, etc.

    How does this balance with the study results? Do fermented foods actually exacerbate this imbalance? Are there ways to selectively increase bacteriodetes organisms?


    justin wrote on November 22nd, 2011
  21. This article makes me wonder something. Clearly antibiotics are a mixed bag I agree. They should be used only when needed. But boy when they are needed they sure are a help. After an illness, should we take a pro-biotic to restore what the anti-biotic has depleted? Is the answer to this problem as simple as that?

    Lorin Partain wrote on November 22nd, 2011
  22. D-Mannose has worked for me for a UTI that 3 rounds of antibiotics wouldn’t kill.

    The antibiotics killed my stomach! But I am feeling better now after taking probiotics for a month.

    carrie wrote on December 2nd, 2011
  23. I know that this is an old post but I saw that Mark was going to follow up with a solutions post. I did a search on the site to see if I could find it to no avail. Can anyone direct me towards the post? Thank you!

    Z wrote on July 5th, 2012
    • Probiotics only ever made me gain weight so if you’re still on those maybe you should quit taking them. They alter your gut flora just like antibiotics and weight gain is a recognized side effect of them now (some people lose weight on them some people gain it). It’s also worth pointing out that weight loss is also now a recognized side effect of antibiotics (in fact some of them are even being suggested as a ‘cure’ for obesity).

      Lila wrote on March 23rd, 2013
  24. Unfortunately, they can’t always be avoided. And I’ve had them three times this year. I’m taking probiotics constantly. I’m on a course now from a bad spider bite and I don’t know what would have happened if I didn’t take them as it made me rather sick.

    Kathy wrote on November 11th, 2012

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