Gut metagenome of tamiasciurus hudsonicus: fecal sample
We used 16s rRNA amplicon sequencing to determine the composition of the gut microbiota from fecal samples. Briefly, microbial DNA was extracted using the Qiagen MagAttract PowerMicrobiome kit (Qiagen, USA) following the manufacturers instructions, and extracted DNA was quantified using the Quant-iT PicoGreen dsDNA assay kit. The hypervariable V4 region of the 16S rRNA bacterial gene was then amplified using a dual-indexing approach to allow for sample assignment after multiplexing [66]. To amplify the V4 region, we used the following primers (forward: GTGCCAGCMGCCGCGGTAA, reverse: GGACTACHVGGGTWTCTAAT, [66]). Following amplification and indexing, libraries were pooled, spiked with PhiX to increase library complexity, and sequenced in two separate runs on an IlluminaMiseq using a MiSeq Reagent Kit V2 (500 cycles) at the University of Michigan Microbiome Core. Each run included 3 positive controls (ZymoBIOMICS Mock Community II) and at least 3 negative controls (H2O).