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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, Simpsons evenness measure E, Shannon diversity index H, Simpsons diversity index, and Faiths 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 BrayCurtis dissimilarity analysis

Antioxid Redox Signal 2018;29:1792807 27

[DOI] [PMC free article] [PubMed] [Google Scholar] 29.Burger-van Paassen N, Vincent A, Puiman PJ, van der Sluis M, Bouma J, Boehm G, van Goudoever JB, van Seuningen I, Renes IB