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Should Antibiotics Be Avoided?

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Without a doubt, antibiotics are one of the most revolutionary medical advances in the history of humanity. Since the widespread use of these drugs began in the mid to late 1940s, countless crippling diseases have been reduced to mere inconveniences, life-changing surgical procedures have become safe and routine, and millions of lives have been saved. And yet, no medication is without side effects. Unfortunately, the widespread availability and impressive effectiveness of antibiotics has resulted in a pervasive complacency about their impact on our bodies and, especially, our gut biome.

Not all antibiotics are created equal. Some work by destroying the cell walls of a narrow range of bacteria. Others inhibit protein synthesis within a wide variety of bacteria, thus preventing them replicating and growing. However, regardless of the mechanism of action or the spectrum of bacteria targeted, every antibiotic has the potential to significantly disrupt your microbiome. Even one short course of antibiotics has been shown to compromise metabolic activity, reduce diversity in the gut, and even promote the growth of harmful antibiotic-resistant organisms. In turn, these dramatic changes to the composition of intestinal microbiota can result in persistent, overwhelming gastrointestinal distress and a leaky gut-blood barrier that allows harmful pathogens to enter the bloodstream.

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Perhaps even more concerning, changes to the gut biome after treatment with a course of antibiotics can be long lasting, sometimes even permanent. In a study published in 2022, 20 healthy volunteers were given one of four different antibiotic treatments over the course of five days. The researchers collected the stool samples at regular intervals from the subjects starting two weeks before the antibiotic treatment course and continuing six months afterward.

Following the short round of antibiotics, it took nearly two months for the majority of subjects to return to baseline values of gut bacteria. Still, the bacterial strains that comprised the gut biome in these subjects remained changed. In fact, for three of the clinical subjects, their microbiota suffered such a drastic loss in compositional quality and diversity that the researchers likened them to those of ICU patients. Ultimately, antibiotic treatments "are fundamentally restructuring the microbiome," states Winston Anthony, one of the coauthors of the study.

Despite these findings and the similar conclusions of other studies, antibiotics continue to have a place in modern medicine. However, some physicians are taking note and prescribing them only when necessary or recommending a daily probiotic for several months after a round of antibiotics to help restore the gut back to good health.


Paul has been interested in medical research since his first organic chemistry class in college. He was a high school biology teacher for 32 years until retiring to spend more time reading, hiking, and camping with his wife and two dogs.


  1. Patangia DV, Anthony Ryan C, Dempsey E, Paul Ross R, Stanton C. Impact of antibiotics on the human microbiome and consequences for host health. Microbiologyopen. 2022 Feb;11(1):e1260. doi: 10.1002/mbo3.1260. PMID: 35212478; PMCID: PMC8756738.
  2. Konstantinidis T, Tsigalou C, Karvelas A, Stavropoulou E, Voidarou C, Bezirtzoglou E. Effects of Antibiotics upon the Gut Microbiome: A Review of the Literature. Biomedicines. 2020 Nov 16;8(11):502. doi: 10.3390/biomedicines8110502. PMID: 33207631; PMCID: PMC7696078.
  3. Mamieva Z, Poluektova E, Svistushkin V, Sobolev V, Shifrin O, Guarner F, Ivashkin V. Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations? World J Gastroenterol. 2022 Mar 28;28(12):1204-1219. doi: 10.3748/wjg.v28.i12.1204. PMID: 35431513; PMCID: PMC8968486.