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The BIOM file output from the DADA2 pipeline and the DECIPHER-aligned FastTree phylogenetic tree were input into QIIME (v1.9.1) and the scripts in the Supplementary Materials (QIIME Scripts compilation) were used to establish the alpha diversity metrics of Chao1 richness estimate, Simpson’s evenness measure E, Shannon diversity index H, Simpson’s diversity index, and Faith’s phylogenetic diversity metric (whole tree) as well as the beta diversity measures of unweighted and weighted UniFrac analyses (the latter of which factors in ASV abundance 37 ) and Bray–Curtis dissimilarity analysis

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And I know this reads like geek speak and may have you feeling like you ARE back in senior year chem class, so let me explain it with an Iron Man analogy