The ecology and evolution of primate phageomes

• Applicant: Dr. Jan Gogarten
• Subject Area: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions ; Evolution, Anthropology ; Microbial Ecology and Applied Microbiology
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 453352748

Every mammal hosts trillions of microorganisms; humans are no exception. These communities constitute a majority of the cells in a host and include bacteria, archaea, microbial eukaryotes as well as many viruses (including bacteria-infecting bacteriophages; hereafter phages). The most abundant and diverse communities are found in the gut and their composition is related to human diseases and long-term mortality risk. Inspired by these insights, researchers increasingly consider the human body as an ecosystem, with health a product of the ecosystem services generated by their microbial communities. Phages have the potential to influence the structure and function of these ecosystems, and ultimately, human health. Despite their potential importance, the ecological and evolutionary processes that gave rise to the modern human phageome remain poorly resolved. Studies of non-human primates have the potential to provide insights into the evolutionary history of the human phageome and the ecological processes that shaped these communities prior to recent modifications in the way humans live (e.g., our highly connected world, use of antibiotics). Anthropogenic disturbance may result in increasing microbial transmission between humans and wildlife, highlighting both the time-sensitivity of this research and the need for strategies to mitigate transmission. This proposal seeks to address these knowledge gaps by studying the gut phageomes of our closest living relatives, non-human primates, while developing phages as a tool to study rates of microorganism transmission at the human-wildlife interface. I will use a rich dataset of chimpanzee fecal samples from 36 populations across Sub-Saharan Africa, including longitudinal samples spanning two decades, as well as from humans and other primates living near these populations. This sample set will allow me to explore the ecological processes shaping wild chimpanzee phageomes and test the hypothesis that chimpanzee phageomes are shaped by their diet, social relationships, environment, and levels of anthropogenic disturbance. Longitudinal sampling will enable the study of phage-bacteria interactions, while broad spatial sampling will facilitate quantification of phage transmission at the human-wildlife interface. I will explore historic processes underlying primate phageome diversity, testing the prediction that larger historic population sizes fostered higher phageome diversity. By comparing primate phageomes with those of African and European human populations, I hope to reveal phages lost to the human lineage and provide an understanding of how phage diversity was shaped by the evolutionary history of the human lineage. The proposed project will provide insights into the ecological and evolutionary processes shaping the diverse and abundant viral communities in the guts of humans and our closest living relatives in our ever changing world.

• DFG Programme: Research Grants
• Co-Investigators: Professor Dr. Sébastien Calvignac-Spencer; Professor Dr. Fabian Leendertz