Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2′-fucosyllactose intake, in adults with overweight or obesity

Antibiotics are widely used to treat bacterial infections, yet overuse and misuse causes disruption of the gut microbiome and spread of antibiotic-resistant bacteria. Presence of antibiotic resistance genes (ARGs) could be a determinant of the response to antibiotics. Supplementation with prebiotics may limit the detrimental antibiotic-induced effects on the microbiome, but whether this results in changes in the gut resistome is unclear. This study investigated the impact of eight-week 2′-fucosyllactose (2′-FL) supplementation after seven-day vancomycin use in 18 adults with overweight/obesity, a subset from a double-blind placebo-controlled randomized intervention. Whole-metagenome shotgun sequencing was used to characterize the gut microbiome and resistome at baseline, after vancomycin use and after supplementation. Seven-day vancomycin use disrupted microbial richness and diversity (p < 0.001) and changed microbial composition. No improvements in microbial recovery were detected after eight week 2′-FL supplementation compared to placebo. Resistome richness and diversity were not affected by vancomycin use, although the presence of specific ARGs changed. No differential impact of 2′-FL supplementation on resistome richness, diversity and composition was detected. While vancomycin use disrupted the gut microbiome and affected the resistome, the detectable effects of 2′-FL supplementation were limited. Future research should investigate antibiotic- and prebiotic-induced changes in the gut resistome in more detail.