160 Chapter 7 V.1.5.2.[7] The assignment of taxonomy was done using the DADA2 implementation of the RDP classifier and SILVA 16S reference database [8, 9]. The α-diversity was assessed by calculating Shannon Diversity Index and ß-diversity was assessed with weighted and unweighted Unifrac, on a rarefied dataset using the phyloseq and microbiome package in R (R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria).
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