Alpha and Beta Diversity Analysis of Baseline and Post-Intervention Samples

The generated RAPID-Dx^® annotation table as well as all associated sample metadata were merged into a Phyloseq version 1.30.0 (McMurdie and Holmes, 2013) object within R 3.6.1 (R Core Team, 2020) for alpha and beta diversity analysis. Annotation counts first underwent internal sequence normalization, in which a per sample quotient of each respective feature by the internal ERCC measure was calculated and then multiplied by a factor of 1,000,000. Observed feature measures were calculated and compared between categorical groups of interest using the Wilcoxon Rank Sum Test and the Holm adjustment using the rstatix package version 0.7.0 (Kassambara, 2020). Principal Coordinates Analysis (PCoA) was performed using the Phyloseq R package on a weighted Jaccard distance matrix. Significance of PCoA clustering was calculated using the adonis test, dispersion was calculated using the betadisper test, and unsupervised fitting of taxa to PCoA ordination was generated using Envfit within the R package Vegan version 2.5-7 (Oksanen et al., 2020). Envfit was run with 999 permutations and species with statistically significant (p<0.001) correlation with the ordination of samples were plotted.