Profiling the effects of rifaximin on the healthy human colonic microbiota using a chemostat model

Rifaximin is a low solubility antibiotic with activity against a wide range of bacterial pathogens. It accumulates in the intestine and is suitable for prolonged use. Three chemostat models (A, B and C) were used to investigate the effects of three rifaximin formulations (, {beta} and {kappa}, respectively) on the gut microbiome. Bacterial populations were monitored by bacterial culture and 16S rRNA gene amplicon (16S) sequencing. Limited disruption of bacterial populations was observed for rifaximin , {beta} and {kappa}. All formulations caused declines in total spores ([~]2 log10 cfu ml-1), Enterococcus spp. ([~]2 log10 cfu ml-1 in models A and C, and [~]1 log10 cfu ml-1 in model B), and Bacteroides spp. populations ([~]3 log10 cfu ml-1 in models A and C, and [~]4 log10 cfu ml-1 in model B). Bacterial populations fully recovered during antibiotic dosing in model C, and before the end of the experiment in models A and B. According to the taxonomic analysis, prior to rifaximin exposure, Bifidobacteriaceae, Ruminococcaceae, Acidaminococcaceae, Lachnospiraceae and Rikenellaceae families represented >92% of the total relative abundance, in all models. Within these families, 15 bacterial genera represented >99% of the overall relative abundance. Overall, the 16S sequencing and culture data showed similar variations in the bacterial populations studied. Among the three formulations, rifaximin {kappa} appeared to have the least disruptive effect on the colonic microbiota, with culture populations showing recovery in a shorter period and the taxonomic analysis revealing the least global variation in relative abundance of prevalent groups.