Antibiotics and gut health

I finally got around to reading Carl Zimmer's highly-recommended National Geographic article about antibiotics and their effect on our microbiome, the "100 trillion microbes that live in our healthy bodies."

Scientists are only now beginning to get answers to those questions. In a paper just published online in the journal Gut, Andres Moya of the University of Valencia and his colleagues took an unprecedented look at a microbiome weathering a storm of antibiotics. The microbiome belonged to a 68-year-old man who had developed an infection in his pacemaker. A two-week course of antbiotics cleared it up nicely. Over the course of his treatment, Moya and his colleagues collected stool samples from the man every few days, and then six weeks afterwards. They identified the species in the stool, as well as the genes that the bacteria switched on and off.

What’s most striking about Moya’s study is how the entire microbiome responded to the antibiotics as if it was under a biochemical mortar attack. The bacteria started producing defenses to keep the deadly molecules from getting inside them. To get rid of the drugs that did get inside them, they produced pumps to blast them back out. Meanwhile, the entire microbiome powered down its metabolism. This is probably a good strategy for enduring antibiotics, which typically attack the molecules that bacteria use to grow. As the bacteria shut down, they had a direct effect on their host: they stopped making vitamins and carrying out other metabolic tasks.

When You Swallow A Grenade



  1. Understanding gut bacteria, even obliquely, will probably be the next big panacea in medicine.  The scope of the problem is certainly daunting, though.  Daunting enough that researchers have accepted limits on their ability to enumerate the organisms, much less even begin to map their interactions, and generally treat the community as a single organism with percentages of gene expression, black-box style.

    Understanding skin bacteria will be the next big cash cow…

  2. When I was a small child, I got a lot of ear infections.  From about ages 2-7, I was prescribed many rounds of penicillin.  By the time I was teen, I couldn’t take penicillin at all (allergic) or any penicillin-like drug.  I would also find out when I had my wisdom teeth removed(age 17) that I can’t take opiates either, or anything opiate-like. 

    Obesity runs through my father’s side of the family.  At 55, I’m unable to lose weight.  When I diet (medically supervised, journaling every bite, with regular exercise, blahblahblah…), I  *gain* weight, as though eating between 1200-1500 cal. (high protein) a day were some sort of signal to my metabolism to go even slower.  Added to this gut problem, I suspect, was three rounds of chemo nine years ago and every other drug that my oncologist added to that toxic soup, *just in case*. Now THAT’S a genade

    I’m looking for answers but have very few avenues left to explore.  I’m cranking out leptin like crazy and was told by an endocrinologist, ‘Yeah, we don’t know what to do with those numbers, though I can tell you your leptin level is high for your weight….. so?’  She was bein’ all uselessly Tough Love.  Me and my spouse will be participating in the American Gut Survey.  If we find, as I suspect we will, that my husband’s gut is much more diverse than mine, I may approach my GI doc for a fecal transplant.  But that is not considered *routine* by any medical insurance company.

      1. The question I’ll be putting to my doc is will my insurance co. object to paying all or part of the costs, if I supply the poop donor and the transplant takes place, say, in the process of doing a routine colonoscopy?  I mean, as long as he’s already there taking a peek…

  3. Guts affect the mind, not just metabolism. The vagus nerve, the peptides, all kindsa nervous system related things going on down there, largely mysterious. Who knows which feelings, leading to thoughts, are steered by those li’l critters down there…

    1. Like a nanobot overmind?  I have ‘The Second Brain’ on my nightstand now; the author, Michael Gershon, is credited with discovering that there are *two* mostly separate and largely independent nervous systems in our bodies.  I’m persuaded at this point to think that if our microbiome does have an effect on one nervous system over another, then it’s the enteric (gut), rather than the brain/spinal cord, and that this rules our thoughts and feelings far more than we’re aware, gut over head rather than the other way round.

  4. I’m on my 3rd bout of antibiotics, too, Aaron.  First Cipro and now Augmentin.  And this bug in my lungs is still lingering.  I bought Kimchi, acidolphilus, 3 qts. of Kefir and 6 lbs. of Greek yogurt.  Good luck with your journey. 

    1. And to you.  I started on garden variety Amoxicillin, moved to something else, and just finished Avelox (Moxifloxacin).

      *** TMI Alert ***

      Oddly enough, the… uh… bowel involvement… only happened once I was finished the moxifloxacin.  I highly recommend it to anyone who has “gastroenteritis” on their bucket list, if you’ll forgive the pun.

  5. I’m one of many thousands who took a Fluoroquinolone – in this case Cipro, who wound up destroyed by the adverse effects which have got to be at least partly to do with gut biome havoc.  I was misprescribed it for a nerve impairment training injury (again like many others).  I didnt work for six months, it physically disabled my musculo-skeletal system, broke down my joints so they audibly crunched and clicked and slipped.  Shut down my digestive system – I lost 16kg in muscle mass over 4 weeks.  And wrecked my peripheral and central nervous system – full blown electrical meltdown, shocks across body, eyes, teeth, acid burning across skin like being plugged into mains socket and a host of other horrific stuff.  The FQ class of antibiotics are for some extremely toxic.  Look up FQ Toxicity.  There are thousands (possibly tens of thousands or more) permanently disabled from this class of antibiotic.  I suspect a lot of people diagnosed with chronic fatigue, ME, PTSD, anxiety etc may well be suffering from FQ toxicities.  Luckily over 2 years on, I’m functional but my former athletic life appears still a long way off since from the start I’m plagued with intense intra cranial pressure headaches which exercise still induces.  If your offered Cipro, Levaquin or Avelox I would steer clear, they operate unlike all other antibiotics. Some of the warnings are on the insert, though you always think you wont be the 1 to 10 in 10,000 they mention.  Perhaps because the real figure is much higher.

  6. OMG  I’m sorry for your misfortunes.  Many doctor’s offices hire P.A.’s who take charge of our health care.  Mine prescribed AMOX first then CIPRO.  It didn’t work.  I demanded to see my DOCTOR and he prescribed AUGMENTIN.  I’m still suffering from a lung infection.  I CAN TASTE the infection.  I’ve got another week to go on these horse pills and am eating loads of Greek Yogurt, Kefir, and prebiotics like Kimchi.  And acidophilus tablets.  Thank you for your post.  

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