Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans

Objectives: The impact of combination antibiotic therapy on the composition of the intestinal microbiota remains ill-defined. We aimed to assess the effect of a 1 week antibiotic regimen on the intestinal microbiota of healthy humans for a period of up to 31 months. Patients and methods: Thirteen healthy adult men received either no treatment or oral broad-spectrum antibiotics (ciprofloxacin, vancomycin and metronidazole) for 7 days. At four timepoints (prior to treatment, on day 9, day 49 and 8-31 months later) faecal samples were collected and analysed using 16S RNA gene sequencing. Results: The short-term impact of broad-spectrum antibiotics on the gut microbiota was profound, with a loss of diversity and drastic shifts in community composition. In addition, antibiotics significantly reduced the abundance of bacterial taxa with important metabolic functions, such as the production of butyrate. The microbiota showed a remarkable return towards baseline after 8-31 months, but community composition often remained altered from its initial state. Conclusions: These findings suggest that combined treatment with vancomycin, ciprofloxacin and metronidazole has a profound and long-lasting effect on microbiota composition, the consequences of which remain largely unknown.