DOI: 10.5061/dryad.c119gm5
title: Data from: Covariation of diet and gut microbiome in African megafauna

description: A major challenge in biology is to understand how phylogeny, diet, and
 environment shape the mammalian gut microbiome. Yet most studies of
 non-human microbiomes have relied on relatively coarse dietary
 categorizations and have focused either on individual wild populations or
 on captive animals that are sheltered from environmental pressures, which
 may obscure the effects of dietary and environmental variation on
 microbiome composition in diverse natural communities. We analyzed plant
 and bacterial DNA in fecal samples from an assemblage of 33 sympatric
 large-herbivore species (27 native, 6 domesticated) in a semi-arid East
 African savanna, which enabled high-resolution assessment of seasonal
 variation in both diet and microbiome composition. Phylogenetic
 relatedness strongly predicted microbiome composition (r = 0.91) and was
 weakly but significantly correlated with diet composition (r = 0.20).
 Dietary diversity did not significantly predict microbiome diversity
 across species or within any species except kudu; however, diet
 composition was significantly correlated with microbiome composition both
 across and within most species. We found a spectrum of seasonal
 sensitivity at the diet-microbiome nexus: seasonal changes in diet
 composition explained 25% of seasonal variation in microbiome composition
 across species. Species’ positions on (and deviations from) this spectrum
 were not obviously driven by phylogeny, body size, digestive strategy, or
 diet composition; however, domesticated species tended to exhibit greater
 diet-microbiome turnover than wildlife. Our results reveal marked
 differences in the influence of environment on the degree of
 diet-microbiome covariation in free-ranging African megafauna, and this
 variation is not well explained by canonical predictors of nutritional
 ecology.
description: Dietary Illumina data Dietary DNA
 metabarcode data. These trnL-P6 metabarcode data are de-multiplexed
 according to sample of origin and provided in fastq format. These files
 represent samples that correspond to sample metadata in Table S1 of the
 manuscript. 20190606_P6Data.tar.gz.txt
 Microbiome Illumina data Microbiome data
 files. These paired-end 16S rRNA data are de-multiplexed according to
 sample of origin and provided in fastq format. These files represent
 samples that correspond to sample metadata in Table S1 of the manuscript.
 The six directories correspond to six libraries sequenced at the MSU core
 facility. Note that sample LM0035 was dropped from further analysis
 because it originated from either one of two Lepus spp.
 20190606_16SData.tar.gz.txt Dietary DNA
 metabarcoding data table: prior to rarefying The
 analysis presented in the paper is based on a rarefied data set in which
 sequence read counts were equalized across samples. This table presents
 the total count of dietary DNA sequences within each sample, prior to
 rarefying. Because rare sequence reads were dropped when rarefying, this
 data table contains more plant taxa than does Table S2. The rows represent
 samples that can be matched to metadata in Table S1; columns are labeled
 with the exact DNA sequence of the plant taxon.
 unrarefied_trnL_P6.csv Microbiome data: prior
 to rarefying The analysis presented in the paper is
 based on a rarefied data set in which sequence read counts were equalized
 across samples. This table presents the total count of microbiome 16S
 sequences within each sample, prior to rarefying. Because rare sequence
 reads were dropped when rarefying, this data table contains more bacterial
 taxa than does Table S3. The rows represent samples that can be matched to
 metadata in Table S1; columns are labeled with the exact DNA sequence of
 the 16S sequence variant. unrarefied_16S.csv