Oral microbiome diversity in chimpanzees from Gombe National Park

Andrew T Ozga,Rebecca S Nockerts,Michael L Wilson,Ian Gilby,Anne C Stone,Anne Pusey

doi:10.1038/s41598-019-53802-1

Andrew T Ozga, Rebecca S Nockerts + Show 4 more

Open Access

https://doi.org/10.1038/s41598-019-53802-1

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Abstract

Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.

Highlights

The human oral cavity contains an estimated 600 different microbial species[1]
We examined sequences from our initial MALT analysis that matched each of these species of plants, animals, and fungi (Supplementary Table 4) and found evidence suggesting that some Neanderthal calculus (Spy[1] and Spy2) contained traces of Ovis aries and calculus from one chimpanzee (13C) contained DNA sequences potentially belonging to Elaeis guineensis (African palm)
We detected five bacterial phyla in the dental calculus of Gombe chimpanzees (Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria) which are commonly found within historic anatomically modern humans (AMH) samples

Summary

Introduction

The human oral cavity contains an estimated 600 different microbial species[1]. The oral microbiome exhibits strong interpersonal and population-specific variation across the globe[2,3], while at the same time differentiating between healthy and diseased oral states[4]. Outside of the oral cavity, within the primate gut, clusters known as ‘enterotypes’ show that regardless of geographic origin, gorillas and chimpanzees share a Prevotella-dominated gut signature with modern humans[16,17,18]. These clusters were generally thought to be associated with the long term dietary practices of the host[17]. This research helps to situate the previously unexplored chimpanzee oral microbiota from dental calculus with other historic and prehistoric human samples in an effort to understand the complexity of microbial diversity across the primate oral ecosystem

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