5. Sequencing Data Analysis
We adapted a previously published pipeline from the R package ‘phyloseq’ for the statistical analysis of our microbial sequence data. Once the sequences were obtained from the sequencing facility, we used the program FastQC to check the initial quality of the sequenced samples and to trim primer sequences from the samples. The quality scores indicated the amount of overlap to use for the merged samples. To keep a minimum phred score of 25, we merged the forward sample at 275 bp and cut the reverse at 225 bp. We used the SILVA v138 reference taxonomy dataset to identify the microbial species present within each sample’s microbial community. Our R script is available on GitHub (https://github.com/rusty-russ/Russell-et-al.-Methods-Paper).