Supplementary Methods
Animal and Sample Collection
Woodrats were collected from Beaver Dam, Washington County, UT, USA on
May 15, 2012. Animals were captured using Sherman live traps baited with peanut butter
and oats, and were immediately transported back to the University of Utah. Plant samples
were collected from the wild using sterile techniques, and immediately frozen. Animals
(2 males, 2 females) were housed individually in shoebox cages with wood shavings, and
fed high fiber rabbit chow (Harlan Teklad 2031) ad libitum. To collect feces, animals
were placed in empty, ethanol-sterilized cages for 2 hour. Feces were immediately
frozen. The University of Utah’s Institutional Animal Care and Use Committee approved
all experimental techniques under protocol 12-12010.
Sequencing
Whole DNA was extracted from all samples using a QIAamp DNA Stool Mini
Kit. A previously established technique was then used to amplify the V4 region of the
16SrRNA gene with the primers 515F and 806R (Caporaso et al., 2011). The reverse
primer also contained a 12 bp barcode sequence, allowed for pooling of samples. PCR
reactions were conducted in triplicate and resulting products were pooled within a
sample. DNA was quantified using Invitrogen’s PicoGreen and a plate reader and cleaned
using the UltraClean PCR Clean-Up Kit (MoBIO). Amplicons were sequenced on an
Illumina MiSeq machine using previously described techniques (Caporaso et al., 2012).
Sequence Analysis
Sequences were analyzed using the QIIME software package (Caporaso et al.,
2010). Sequences underwent standard quality control and were split in to libraries using
default parameters in QIIME. Sequences were grouped into operational taxonomic units
(OTUs) using UCLUST (Edgar, 2010) with a minimum sequence identity of 97%. The
most abundant sequences within each OTU were designated as a ‘representative
sequence’, and then aligned against the Greengenes core set (DeSantis et al., 2006) using
PyNAST (Caporaso et al., 2009) with default parameters set by QIIME. A PH Lane mask
supplied by QIIME was used to remove hypervariable regions from aligned sequences.
FastTree (Price et al., 2009) was used to create a phylogenetic tree of representative
sequences. OTUs were classified using the Ribosomal Database Project (RDP) classifier
with a the standard minimum support threshold of 80% (Wang et al., 2007). Sequences
identified as chloroplasts or mitochondria were removed from analysis. Any operational
taxonomic unit (OTU) that contained less than 10 sequences was also removed from
analysis (Bokulich et al., 2013)
Several  diversity measurements were calculated for each sample. We calculated
the Shannon Diversity Index, a biodiversity measure that incorporates both richness and
evenness. We calculated evenness, or how similar in abundance the OTUs in a sample
are, as well as Chao1, which estimates the asymptote on a species accumulation curve to
estimate OTU richness. However, these diversity metrics weight all OTUs equally
regardless of phylogenetic relationships. Therefore, we calculated a measurement of
phylogenetic diversity (Faith, 1992), which measures the cumulative branch lengths from
randomly sampling OTUs from each sample. For each sample, we calculated the mean of
20 iterations for a sub-sampling of 69,334 sequences.
We compared community memberships (presence or absence of lineages, and not
their relative abundances) of treatment groups. We calculated unweighted and weighted
UniFrac scores, which measures diversity shared between treatment groups ( diversity)
by determining the fraction of branch length shared between two samples in the
phylogenetic tree created from all representative sequences. We then conducted Principal
Coordinates Analysis (PCoA) on these data.
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