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Disclosing the ecological and evolutionary origins of primate-associated bacteriophage communities

We live in a world dominated by viruses; those causing disease in humans are painfully familiar to us, but little is known about most viruses harbored within a person, what scientists refer to as ‘viral dark matter’. The majority of these human-associated viruses are actually phages that infect bacteria in the gut. To determine the origins of the phage communities in the human gut, Drs. Jan Gogarten, Fabian Leendertz, and Sébastien Calvignac-Spencer of the Robert Koch Institute led an international research effort to describe the phages of our closest living relatives, non-human primates. The comparative study examined the gut phages in 23 wild primate species living in very different ecosystems across the globe, as well as from humans living in Europe and Africa. The results have been published in the journal PNAS (

Grooming chimpanzees in Taï National Park. Source: Roman Wittig/Tai Chimpanzee ProjectGrooming chimpanzees in Taï National Park Source: Roman Wittig/Tai Chimpanzee Project

Surprisingly, they found relatives of most human associated phages in wild primates. When they looked at the evolutionary relationships of these phage lineages, they found that for many, the relationships of phages were a near mirror image of the evolutionary history of the primates. This pattern of co-divergence suggests that some phages maintained an association with specific primate lineages over millions of years.

They also found that neighboring social groups of baboons harbored unique phage communities, with close grooming partners having more similar phage communities, even after controlling for similarities in the baboon’s bacterial communities and the genetic relationship of the baboons. The team set out to understand how flexible the association of primates and their phages are by studying the phages of primates in zoos, as well as the phages of their zookeepers. Captive primates lost the phages they normally harbor in the wild, with those phages all replaced by human-associated ones.

This study provides insights into the evolutionary and ecological origins of our associated ‘viral dark matter’ and opens up exciting avenues of research. It suggests phages can serve as a marker of microbial transmission at the human wildlife interface, providing a much-needed tool to identify high-risk areas for pathogen transmission.

This study was a collaborative effort with scientists in Germany working at the Robert Koch Institute, Christian-Albrecht-University of Kiel, the Max Planck Institute for Evolutionary Biology, and the Max Planck Institute for Evolutionary Anthropology, as well as colleagues from the University of Neuchatel in Switzerland, the Université Alassane Ouattara de Bouake in the Côte d’Ivoire, the National Institute for Biomedical Research in the Democratic Republic of the Congo, and the University of Notre Dame, Duke University, and Harvard University in the USA.

Date: 07.04.2021


  • Gogarten JF, Rühlemann M, Archie E, Tung J, Akoua-Koffi C, Bang C, Deschner T, Muyembe-Tamfun JJ, Robbins MM, Schubert G, Surbeck M, Wittig RM, Zuberbühler K, Baines JF, Franke A, Leendertz FH, Calvignac-Spencer S (2021): Primate phageomes are structured by superhost phylogeny and environment.
    Proc. Natl. Acad. Sci. U. S. A. 118 (15): e2013535118. Epub Apr 5. doi: 10.1073/pnas.2013535118. more