PT  - JOURNAL ARTICLE
AU  - Moura, Ines B.
AU  - Buckley, Anthony M.
AU  - Ewin, Duncan
AU  - Clark, Emma
AU  - Mitra, Suparna
AU  - Wilcox, Mark H.
AU  - Chilton, Caroline H.
TI  - Profiling the effects of rifaximin on the healthy human colonic microbiota using a chemostat model
AID  - 10.1101/828269
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 828269
4099  - http://biorxiv.org/content/early/2019/11/01/828269.short
4100  - http://biorxiv.org/content/early/2019/11/01/828269.full
AB  - 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 (α, β and κ, 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 α, β and κ. 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 κ 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.