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).