27Rifaximin is a low solubility antibiotic with activity against a wide range of bacterial 28 pathogens. It accumulates in the intestine and is suitable for prolonged use. Three chemostat 29 models (A, B and C) were used to investigate the effects of three rifaximin formulations (α, β 30 and κ, respectively) on the gut microbiome. Bacterial populations were monitored by 31 bacterial culture and 16S rRNA gene amplicon (16S) sequencing. Limited disruption of 32 bacterial populations was observed for rifaximin α, β and κ. All formulations caused declines 33 in total spores (~2 log10 cfu ml -1 ), Enterococcus spp. (~2 log10 cfu ml -1 in models A and C, 34 and ~1 log10 cfu ml -1 in model B), and Bacteroides spp. populations (~3 log10 cfu ml -1 in 35 models A and C, and ~4 log10 cfu ml -1 in model B). Bacterial populations fully recovered 36 during antibiotic dosing in model C, and before the end of the experiment in models A and B. 37According to the taxonomic analysis, prior to rifaximin exposure, Bifidobacteriaceae, 38 Ruminococcaceae, Acidaminococcaceae, Lachnospiraceae and Rikenellaceae families 39 represented >92% of the total relative abundance, in all models. Within these families, 15 40 bacterial genera represented >99% of the overall relative abundance. Overall, the 16S 41 sequencing and culture data showed similar variations in the bacterial populations studied. 42 Among the three formulations, rifaximin κ appeared to have the least disruptive effect on the 43 colonic microbiota, with culture populations showing recovery in a shorter period and the 44 taxonomic analysis revealing the least global variation in relative abundance of prevalent 45 groups. 46 Rifaximin is an oral antibiotic with low solubility and in vitro bactericidal activity reported 48 against a wide range of facultative and obligate aerobes such as, Escherichia coli, 49 Clostridioides difficile, Staphylococcus spp., and Streptococcus spp., among others [1-3]. Its 50 chemical structure is a derivative of rifamycin and contains a supplementary pyridoimidazole 51 ring that limits the absorption of the drug in the intestine [3]. Rifaximin is considered suitable 52 for prolonged use due to its poor solubility and subsequent low systemic side effects [2, 4]. It 53 is FDA approved for the treatment of traveller's diarrhoea and irritable bowel syndrome 54 (IBS), and has been shown effective in clinical trials as therapeutic agent in small bowel 55 bacterial overgrowth, inflammatory bowel disease and in C. difficile infection [2, 4-8]. 56 Rifaximin is also used to reduce the risk of hepatic encephalopathy in patients with impaired 57 liver function and portosystemic shunting [9]. 58 A decline in colonic bacterial diversity has been reported during rifaximin use, [10-12] with 59 bacterial populations recovering following antibiotic treatment. However, studies have 60 mostly investigated variations in faecal samples from particular patient groups with 61 gastrointestinal or immune diseases [10, 12-14], who may already have a depleted gut 62 microb...