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A Healthy Microbiome Buffers Against the Effect of Antibiotics

Written by Charlotte Harrison, Science Writer 

Antibiotics are crucial treatments for bacterial infections. However, antibiotic exposure can lead to changes in the host microbiome and select for antibiotic resistance genes in commensal and pathogenic bacteria. 

Researchers from Washington University School of Medicine have published a study in Cell Reports that investigated how antibiotics change the microbiome of healthy individuals. The study aimed to improve upon previous research into antibiotic–microbiome interactions that are largely performed in hospitalized patients, which can confound results. 

The authors used quantitative microbiologic culture and metagenomic sequencing to quantify microbiome dynamics from 20 individuals before, during, and 6 months after four antibiotic treatment regimens commonly used for community-associated pneumonia. The antibiotics were azithromycin, levofloxacin, cefpodoxime, and a combination of azithromycin and cefpodoxime, all of which were administered orally for 5 days. The microbiomes of volunteers treated with these antibiotics were compared with the microbiomes of hospitalized patients. 

Microbiome recovery but long-term effects 

The researchers found that each antibiotic treatment had a remarkably similar effect on the microbiome. Antibiotic treatment caused an acute decrease in species richness and culturable bacteria. The microbiome of the majority of study participants returned to pre-treatment species richness (that is, taxonomic diversity) after 2 months. But this recovery was associated with an altered taxonomy, increases in the expression of antibiotic resistance genes, and increased metabolic output. The authors note that these changes imply that antibiotic treatment has long-term consequences. 

Moreover, treatments that contained azithromycin had a slower recovery of species richness. 

Individuals at-risk of perturbation 

Three study participants who had low microbiome diversity at the start of the study had a persistent reduction in microbiome diversity after antibiotic treatment. Indeed, the composition of their microbiomes shared compositional similarities with hospitalized patients.  The authors note that this result shows that a single dose of antibiotics can lead to long-term microbial perturbation in healthy individuals 

The study had several limitations: the short-read shotgun metagenomic DNA sequencing could not determine what microbiota functions are actively expressed, plus the study had a small number of participants. Nevertheless, this paper shows that the healthy microbiome buffers antibiotic-specific changes to the relative abundance of specific bacterial taxa, and suggests that identifying individuals at greater risk of microbiome perturbation should be a key area of future research. 

Image Credit: Canva

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Antibiotics / Microbiome

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