A group of wild-type C3H/HeOuJ background mice were treated with antibiotic containing water ad libitum or control group was given standard drinking water. Antibiotic treatment consisted of neomycin and polymyxin B (final concentrations: 0.6 mg/mL for neomycin and 120 units/mL for polymyxin B, both from Sigma-Aldrich, St. Louis, MO, United States) given in drinking water for 8 weeks as described earlier (Prakash et al., 2015 (link)). This combination of antibiotics was chosen specifically for the ability of both to remain within the gut and not be absorbed into circulation; by using this combination to target the gut microbiome, we could focus primarily on its effects without disruption of other microbiomal niches. Supplementary Figure S6 demonstrates the effects of this combination on the richness, evenness, and diversity of the microbiome after 7 weeks of treatment.
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