The Effects of Antibiotics on Gut Flora

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The Effects of Antibiotics on Gut Flora

How big a deal is one round of antibiotics?

According to this article, with some antibiotics, it’s enough to disrupt your gut flora for a whole year

For months after taking a full course of ciprofloxacin, clindamycin, amoxicillin or minocycline, participants were found to have decreased bifidobacillus, the organisms that produce butyrate (food for the colon, helping to prevent colon cancer and helpful to heal up any kind of inflammation in the colon, like Crohn’s and Ulcerative Colitis).

Diversity of gut flora also declined for up to 12 months with cipro (not surprising because that’s like the nuclear warhead of antibiotics).

Amoxicillin (in the penicillin family) didn’t affect diversity much, but it did lead to antibiotic resistant genes in the bacteria.

Why Diversity Matters

Why does diversity matter? For the same reason you shouldn’t marry your cousin: diversity creates a sort of checks-and-balances system that prevents a single genetic weakness from wreaking havoc. Less diversity leads to a more tenuous balance, and greater susceptibility to illness.

Your gut, we are realizing more and more, is the gateway not just to pathogenic illnesses, but also to noninfectious gut disorders like allergies and autoimmunity. It’s also the key to protecting against these ailments.

Why Antibiotic Resistance Matters

Microbes adapt to their environments just like we do. Their goal is to survive, just like ours is. It’s essentially a war. How long it takes for bacteria to develop resistance to an antibiotic depends on how long and how often that bacteria is exposed to a drug.

At this point, according to the CDC, bacteria are now becoming resistant to the drugs we have faster than we can create new drugs to which they haven’t yet adapted. This is partly because of over-prescribing, and partly because we’re not coming out with new antibiotics nearly as often as we used to. (Antibiotics, which are prescribed for short courses only, are less profitable for drug companies than drugs people might be expected to stay on long term. The CDC guy said it, not me.)

This is why it’s important to save the “big guns” (like cipro) for cases that really need it… and to limit the prescription of antibiotics in general only to cases that truly require them.

More often than not, some heavy duty immune support (food, supplements, fasting, sleeping more) is all it takes!


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By |2017-05-30T07:34:01-07:00January 8th, 2016|Categories: Articles, Conditions & Treatments|Tags: |1 Comment

About the Author:

Dr. Lauren Deville is board-certified to practice medicine in the State of Arizona. She received her NMD from Southwest College of Naturopathic Medicine in Tempe, AZ, and she holds a BS in Biochemistry and Molecular Biophysics from the University of Arizona, with minors in Spanish and Creative Writing. She also writes fiction under a pen name in her spare time. Visit her author website at

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  1. […] unnecessary antibiotics, as this can create low biodiversity, shifting the ratio in favor of […]

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