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\cite{Caporaso_2012}.  ##Bioinformatic Analysis  Unless otherwise noted, all microbial community analyses were conducted using the QIIME workflow version 1.8, and all 1.8 or R All  python scripts referred to are components of QIIME \cite{Caporaso_2010}. ###Demultiplex and QC.  An in-house script was used to assign sequences to samples, using dual-index barcoding. This script is available on github (https://github.com/gjospin/Demul_trim_prep)  ###OTU assignment and QC