Fig. 2: Temporal stability of plasma metabolites.

a, Principal component analysis of metabolite levels at two time points (Euclidean dissimilarity). The green dots indicate baseline samples and the orange dots indicate follow-up samples (n = 311 biologically independent samples). The Kruskal–Wallis test (two sided) was used to check differences between baseline and follow-up. b, Temporal stability of metabolites stratified by the dominantly associated factor for each metabolite. The Wilcoxon test (two sided) was used to check the differences between groups. Each dot represents one metabolite. The y axis indicates the Spearman correlation coefficient of abundances of each metabolite between two time points (n = 311 biologically independent samples). In a and b, the box plots show the median and first and third quartiles (25th and 75th percentiles) of the first and second principal components (a) or correlation coefficients (b); the upper and lower whiskers extend to the largest and smallest value no further than 1.5× the interquartile range (IQR), respectively; and outliers are plotted individually. c, Correlation between metabolite stability and the metabolite variance explained by diet (left), genetics (middle) and the microbiome (right). The x axis indicates the inter-individual variation explained by each factor and the y axis indicates the Spearman correlation coefficient (two sided) of abundances of each metabolite between the two time points. The dashed white lines show the best fit and the gray shading represents the 95% confidence interval (CI) (n = 311 biologically independent samples).