Abstract
The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. Here we use 16S rRNA sequencing to characterize the microbiota of wild western lowland gorillas and sympatric central chimpanzees and demonstrate compositional divergence between the microbiotas of gorillas, chimpanzees, Old World monkeys, and modern humans. We show that gorilla and chimpanzee microbiomes fluctuate with seasonal rainfall patterns and frugivory. Metagenomic sequencing of gorilla microbiomes demonstrates distinctions in functional metabolic pathways, archaea, and dietary plants among enterotypes, suggesting that dietary seasonality dictates shifts in the microbiome and its capacity for microbial plant fiber digestion versus growth on mucus glycans. These data indicate that great ape microbiomes are malleable in response to dietary shifts, suggesting a role for microbiome plasticity in driving dietary flexibility, which may provide fundamental insights into the mechanisms by which diet has driven the evolution of human gut microbiomes.
Highlights
The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts
To characterize microbiotas of wild African great apes, we sequenced the V1–V3 region of the bacterial 16S rRNA gene in fecal samples collected from 87 individual western lowland gorillas (WLGs) (Fig. 1a) and 18 sympatric chimpanzees (Supplementary Data 1-3) from the Sangha region of the Republic of the Congo (Fig. 1b, Supplementary Note 1) over 2008–2010
The most striking difference in WLGs compared to humans and other non-human primates (NHPs) is the highrelative abundance of the phylum Chloroflexi
Summary
The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. Metagenomic sequencing of gorilla microbiomes demonstrates distinctions in functional metabolic pathways, archaea, and dietary plants among enterotypes, suggesting that dietary seasonality dictates shifts in the microbiome and its capacity for microbial plant fiber digestion versus growth on mucus glycans. Human studies from various populations have suggested that the relative abundance of core bacterial taxa in intestinal microbiomes of individuals varies widely and that individuals cluster within two to three stratified variants or “enterotypes” defined by Bacteroides, Prevotella, or Ruminococcus[6,7,8,9,10] These enterotypes, or stratified clusters within a population defined by microbiota composition, are linked to long-term dietary patterns[8]. Environmental instability may be conceptually important, as functional variations between compositionally distinct gut microbial communities may have facilitated adaptation of early primates to changing nutritional resource availability[19]
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