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.