Sample Collection and Processing
Fresh fecal samples were collected from 17 captive-born captive chimpanzees during their transport from the New Iberia Research Center, Louisiana, USA to Project Chimps Sanctuary, Georgia, USA in March and September of 2018. Samples were immediately stored at -20°C then transferred to -80°C within one month. DNA was extracted using DNeasy PowerSoil PowerLyzer DNA Extractions kits according to the manufacturer’s protocol. Amplicons of the V4-V5 regions of the 16S rRNA gene were generated using 515F/926R primers based on the Earth Microbiome Project (EMP) 16S Illumina Amplicon protocol (Thompson et al. 2017). Amplicons were sequenced on an Illumina MiSeq platform using V3 chemistry and 2×250 bp paired-end reads at the Weill Cornell Medicine Microbiome Core Lab following methods of the EMP.