2.6. Statistical analyses
Statistical analyses were performed using R (v3.5.1) software packages. Shannon diversity indices and Bray-Curtis dissimilarity indices were respectively computed by the functions diversity andvegdist in the vegan R package. Two-sided Wilcoxon’s rank-sum test was used for comparisons of Shannon diversity and Bray-Curtis dissimilarity indices between two groups. Two-sided Fisher’s exact test was used to compare the occurrence of antibiotic resistance genes. Principal coordinates analysis (PCoA) was performed using thedudi.pco function in the ade4 R package. The species and gene family signatures were identified using LEfSe.21Briefly, Kruskal-Wallis rank-sum test was used to detect features with significantly differential abundance between two groups. LEfSe then applied linear discriminant analysis (LDA) on these features to estimate their effect sizes in delineation between different disease states. For all boxplots, the box edges denoted the first and third quartiles and the horizontal line denoted the median, with the whiskers extending up to the 1.5-fold interquartile ranges.