16S v4 of Sciurus carolinensis feces
Using QIAamp DNA Stool Mini Kits (Qiagen, Hilden Germany), we extracted bacterial DNA from 0.2 g subsamples of faecal samples, which in other rodents are indicative of bacterial communities in the large intestines [116]. Extracts underwent triplicate PCR amplification of the 16S rRNA gene v4 region (515F-806R modified primers; Walters et al. 2015) at MetaGenomBio Inc (Toronto Canada) alongside pcr negative controls. Triplicate PCR products were then pooled prior to sequencing on an Illumina MiSeq using v2 chemistry (250bp read).