Molecular Methods
We isolated DNA from fecal samples stored on Whatman FTA Cards using the
Qiagen DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany) following the
manufacturer’s extraction protocol. We included six blank negative
controls to account for possible contamination during extraction and
polymerase chain reaction (PCR). Following standardized procedures
(Caporaso et al. 2012), we used PCR to amplify the V4 region of
the 16S microbial small subunit ribosomal RNA (rRNA) gene using the
Earth Microbiome Project universal primers 515f/816r. We then used the
Illumina MiSeq sequencing platform to obtain paired-end 150 base pair
reads. DNA extractions took place at the Field Museum of Natural
History. All subsequent molecular work was conducted at the IGM Genomics
Center of the University of California, San Diego.