Antibiotics and the human microbiome

Antibiotics and the human microbiome


First off, antibiotics are a miracle of modern medicine. They’ve saved hundreds of millions, if not billions, of lives over the last century. It used to be, a long time ago, if you got a paper cut and that got infected, that could be the end of your life. Right? We don’t live in that world anymore, and it’s a better world to live in to not be dying of infectious disease constantly. So antibiotics are great. They’re a godsend. They’re wonderful. However, there’s been a cost to antibiotics that has been underappreciated over the past century or so that we’re just now beginning to understand. One of those costs we’ve known for a long time, which is the rise of antimicrobial resistance. Genes that are resistant to antibiotics … I should back up a bit. Antibiotics that we use in medicine, they already existed in the natural world for millions and millions of years. These are chemicals that microbes use for warfare against one another. Genes that resist these antibiotics already exist in the soil, or in the water, or what have you. When we start using high doses of antibiotics in humans, those pathogens that are infecting humans will eventually find their way to one of the Solen bacteria, for example, that might contain one of these antimicrobial resistance genes for that antibiotic and transfer it to the pathogen. Bacteria are notoriously promiscuous when it comes to transferring DNA across each other. On our level, it would be unthinkable for a banana tree and a zebra to mate, but in the microbial world, organisms that are equivalently distant can actually exchange genetic material. With the use of antibiotics, we’ve seen the influx of these pre-existing resistance genes out in the world or through the evolution of these resistant organisms. That’s the first cost. The next big cost that we didn’t really think about very much in the beginning was the depletion of our indigenous microbiota. Antibiotics are a scorched-earth policy. Broad spectrum antibiotics, they’re not just hurting the bad bug that’s infecting you, but they’re also killing off a lot of the native microbes that are in and on your body. This can leave you even more vulnerable after having taken them to other types of infections or secondary infections and so on. Over long spans of time, over generations, we actually see a slow and steady loss of microbial diversity, some of which is potentially passed from mother to child, in a venting of this diversity and a loss of the ecology of our bodies. In the Western world, we have seen a mild uptick in certain autoimmune disorders, overactive immune system-type disorders that seem to be associated with use of antibiotics, changes in our diet, eating less fiber, for example, and a steady loss of microbial diversity in our bodies. I think the answer is don’t be afraid to use antibiotics. If you need antibiotics, please use antibiotics. You shouldn’t not use antibiotics. If you have a viral infection, don’t use antibiotics, of course. You need to be responsible about your use of antibiotics, but what we need to think about for the next generation of treating people with these drugs is how do we recolonize or recover a healthy microbiome following antibiotics treatment? There are a few ways to think about this. I know there are groups working on these pills you can swallow that have a capsule on the outside that only dissolves in the lower colon that contain activated carbon. This can kind of soak up the antibiotic in the colon and actually prevent it from killing off your gut microbiota. That’s a way of sort of resisting the killing of microbes of an antibiotic treatment. Then you could also have a recovery side where there are these things called autologous fecal transplants. We’ll probably get to that later on in our conversation. Which, in that autologous just means from yourself. So I could take my poop, and I could put it in the freezer when I’m healthy, and store it for a rainy day. Down the road I get antibiotic treatment and at the end of that treatment, I can take a poop pill of my own poop and recolonize my own gut with my healthy microbes from before as a way to bring back that diversity after the treatment. I think the future of medicine will incorporate these other treatments that actually help us to maintain and regenerate the microbial diversity that we initially had even after these antibiotic treatments.

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