Narrow- and broad-spectrum antibiotics treatment dramatically alters the intestinal bacterial, viral and metabolomic composition of healthy volunteers
Over the last century, antibiotics have dramatically decreased infection-associated deaths, but have also had the unintended consequence of disrupting human commensal bacterial communities and selecting for pathogens with antibiotic resistance. The intestinal microbiota and its metabolic products are increasingly recognized to mediate critical roles in human development, health, and disease, and an improved understanding of the microbial and metabolic consequences of antibiotic treatments is greatly needed. Here, we analyzed the bacteriome, virome, and metabolome in stool samples collected from 63 healthy adult volunteers treated with narrow- or broad-spectrum antibiotics or serving as controls. We found that while narrow- and broad-spectrum antibiotics treatment both significantly altered the intestinal bacteriome, virome and metabolome, massively disrupting the endogenous community landscape, they did so in differential ways. We report antibiotic class-dependent alterations in microbiota function, supported by associations between bacterial taxa and metabolites. Finally, we reveal treatment-specific modulation of the genomic reservoirs of antimicrobial resistance. These findings provide much-needed insights into the consequences of different antibiotic regimens and will serve as a valuable resource for development of targeted interventions to limit the detrimental side effects of these life-saving drugs.
Over the last century, antibiotics have dramatically decreased infection-associated deaths, but have also had the unintended consequence of disrupting human commensal bacterial communities and selecting for pathogens with antibiotic resistance. The intestinal microbiota and its metabolic products are increasingly recognized to mediate critical roles in human development, health, and disease, and an improved understanding of the microbial and metabolic consequences of antibiotic treatments is greatly needed. Here, we analyzed the bacteriome, virome, and metabolome in stool samples collected from 63 healthy adult volunteers treated with narrow- or broad-spectrum antibiotics or serving as controls. We found that while narrow- and broad-spectrum antibiotics treatment both significantly altered the intestinal bacteriome, virome and metabolome, massively disrupting the endogenous community landscape, they did so in differential ways. We report antibiotic class-dependent alterations in microbiota function, supported by associations between bacterial taxa and metabolites. Finally, we reveal treatment-specific modulation of the genomic reservoirs of antimicrobial resistance. These findings provide much-needed insights into the consequences of different antibiotic regimens and will serve as a valuable resource for development of targeted interventions to limit the detrimental side effects of these life-saving drugs.
amsterdam university medical center - location amc