Microbiome and Metabolome Analysis

All statistical analyses were performed in R software (V 2.15.3) (R Foundation for Statistical Computing, Vienna, Austria) and IBM SPSS 20.0 (IBM Corporation, USA). Analysis of variance (ANOVA) and multiple comparison analysis was applied to calculate the mean and standard deviation and for statistical tests. The differences of parameter variance were estimated by ANOVA and the Kruskal Wallis rank-sum test based on the distribution of parameter statistics. For post-hoc comparison, Tukey’s honest significant differences tests and Wilcoxon matched-pairs signed-rank test were applied. R (V 3.2.2) was employed to perform heat map, PCoA, and hierarchical clustering. The R language did a comparison of microorganisms through the ‘adonis’ function from R’s ‘vegan’ package. The multiple null hypothesis testing of the prior group was achieved using the ‘anosim’ or ‘adonis’ function from R’s ‘vegan’ package. According to the method of Franzosa et al. [52 (link)], we clustered the differentially abundant features via a custom approach. Then, the correlation analysis of the differentially abundant chemical components with the differentially abundant microorganisms was undertaken (For all clustering analyses, we applied Spearman’s rank correlation as a similarity measure with a threshold of r = 0.7). Unless otherwise stated, the significance level was set at p < 0.05.