Figure 1. COPRO-Seq analysis of the structure of a 12-member artificial human gut microbial community as a function of diet and time.

(A) The 12 bacterial species comprising the artificial community. (B) Principal coordinates analysis (PCoA) was applied to relative abundance data generated by COPRO-Seq from two experiments (E₁, E₂), each spanning 6 wk. Following colonization (day 0), mice were switched between two different diets at 2-wk intervals as described in Figure S3. COPRO-Seq data from E₁ and E₂ were ordinated in the same multidimensional space. For clarity, only data from E₂ are shown here (for the E₁ PCoA plot, see Figure S5A). Red/blue, feces; pink/cyan, cecal contents. (C) Proportional abundance data from E₁ illustrating the impact of diet on fecal levels of a diet-sensitive strain with higher representation on HF/HS chow (B. caccae), a diet-sensitive strain with higher representation on LF/HPP chow (B. ovatus), a diet-insensitive strain with no obvious diet preference (B. thetaiotaomicron), and a diet-sensitive strain with a preference for the LF/HPP diet that also achieves a high level of representation on the HF/HS diet (B. cellulosilyticus WH2). Mean values ± SEM are shown. Plots illustrating changes in abundance over time for all species in both experiments are provided in Figure S4C.