Fig. 4

The tri-stable-switch circuit helped the gut microbiota of mice recover from the effects of excess lactose intake. a The design of the murine experiment for gut microbiota profiling. b Top panel: The gut microbiota composition of individual mice in the untreated group (n = 58), model group (n = 59), control group (n = 53), and test group (n = 55) plotted on a principal coordinate analysis (PCoA) using Jensen-Shannon Divergence (JSD). Bottom panel: The gut microbiota samples are plotted according to their collection date on the y-axis over 21 days, and their position on the x-axis is plotted according to their first principal coordinate in the JSD PCoA. A Loess regression is applied to these points using the collection date and principal coordinate 1 (PCo1) coordinates, and the curves are plotted in different colors according to their groups, with the 95% pointwise confidence interval band shaded gray. c The PCo1 coordinates (mean ± S.E.M.) from the four trial groups across 21 days. * P < 0.05, ** P < 0.01, *** P < 0.001; n.s., not significant. Mann-Whitney-Wilcoxon test. d The network was constructed using unweighted adjacency matrices produced by SPIEC-EASI. Sparse inverse covariance estimation based on glasso determined whether there was a correlation in abundance between the two amplicon sequence variants (ASVs), indicated by the gray edge. The size of the node represents the mean abundance calculated using different subsets of samples (defined in the “Results” section and “Methods” section). The color of the node represents the class level that the ASV is classified as. e Top panel: The boxplot displays the differences in Bacteroides abundance among the three data subsets in d. *** P < 0.001; n.s., not significant. Mann-Whitney-Wilcoxon test. Bottom panel: Each of the points represents the Bacteroides abundance of one sample from the four groups defined in a. A Loess regression was applied to these points, and the curves are plotted in different colors according to their groups, with the 95% pointwise confidence interval band shaded gray