Bacterial community analysis
The QIIME2 bioinformatics pipeline (Data analysis and visualizations were carried out in R studio (Version R 3.6.1), using the phyloseq, vegan, ggplot2, gridextra, and scales packages. The α diversity metrics were calculated and significance of multiple continuous variables determined using the Pairwise Wilcoxon test with Bonferroni adjustment. The Wilcoxon test with False Discovery Rate (FDR) algorithm was used when comparing categorical variables. The β diversity was assessed using weighted Bray–Curtis dissimilarities and displayed using PCoA analysis and PERMANOVA was used to determine the significance of dissimilarity between groups.