Rarefaction
Rarefaction of microbial data to normalize for varying library size can
lead to data loss and may be detrimental to interpretation of results
(McMurdie and Holmes 2014). To ensure that patterns observed in
non-rarefied data are not due to bias in library size, we rarefied all
libraries to 7,000 reads. We then conducted alpha and beta diversity
analyses, described below. Results from rarefied tests did not
qualitatively differ from the non-rarefied data (Figure S1). In the main
text, we present and discuss the results of non-rarefied data.