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.