Combining NHP and human data for meta-analyses
Raw FASTQ sequence files and metadata from the captive chimpanzee samples were uploaded to the public database Qiita (Gonzalez et al. 2018) as study ID 12140 and processed using the database’s implementation of the Quantitative Insights Into Microbial Ecology (QIIME2) software. We combined our data from captive chimpanzees (Pan troglodytes subspp. ) retired from the New Iberia Research Center (USA2) with gut microbiota 16S rDNA datasets from wild chimpanzees (Pan troglodytes schweinfurthii ) (n = 96) from Tanzania (Moeller et al. 2016b) (TZA), wild chimpanzees (P. t. troglodytes ) (n = 18) and gorillas (Gorilla gorilla gorilla ) (n = 28) from the Democratic Republic of the Congo (DRC), captive chimpanzees (P. t. subspp. ) (n = 18) and gorillas (G. g. subspp. ) (n = 15) from the United States (USA1) (Campbell et al. 2020), wild red-shanked doucs (Pygathrix nemaeus ) from Vietnam (VNM) (n = 66), and captive red-shanked doucs (P. n. ) from Singapore (SGP) (n = 15) and the United States (USA) (n = 12) (Clayton et al., 2016). This combined wild and captive NHP gut microbiota dataset was then merged with a dataset from humans (n = 528) living in the USA (Yatsunenko et al. 2012). Forward and reverse sequences were demultiplexed and quality filtered using default settings. High-quality reads were trimmed to equal length and amplicon sequence variants (ASVs) were identified using Deblur. Data were rarefied to 10,000 sequences per sample and exported from Qiita for analyses in QIIME2 v 2018.11 (Boylen et al. 2019).