Medication disrupts human gut microbiome

Exposure to single or multiple drugs can have extensive disruptive effects on the human gut microbiome, a new study has found.

Using a shotgun metagenomic approach, researchers assessed the microbiota profiles of faecal samples collected from 4,198 participants (mean age 66.4 years, 59 percent men) of the Japanese 4D project. Second faecal samples were also retrieved from 243 participants after medication initiation and discontinuation. A total of 759 drugs were included in the analysis, along with other metadata such as diet, lifestyle, and comorbidities.

On average, each participant took 5.1 drugs, with 87.0 percent of the study sample taking at least one medication. Proton pump inhibitors (PPIs) and dihydropyridine derivatives were the most common class of drugs.

Of all metadata assessed, medications had the strongest explanatory power for variations in the microbiome. It could account for 10.4 percent of the total variance in gut microbiota at the genus level, and 5.0 percent at the species level.

In particular, medications for the alimentary tract and for diabetes, as well as anti-infective drugs for systemic use, had strong impacts on the gut microbiome. The same was true for PPIs, osmotic laxatives, alpha-glucosidase inhibitors, aspirin and other platelet aggregation inhibitors, and HIV antivirals.

“We have unveiled extensive effects of individual and multiple drugs (polypharmacy) on the gut microbiome, using both a large-scale metagenomic dataset collected from 4,198 deeply phenotyped individuals and a two-time points dataset collected before and after taking drugs,” the researchers said.

“We anticipate that the drug–microbe associations identified in this study could serve as a catalogue, forming a basis for future pharmacomicrobiomics to improve therapeutic effectiveness and reduce adverse drug events that may result from modifications to the gut microbiome,” they added.