This repository holds all scripts used in the data processing and analysis of the Article "Functional host-specific adaptation of the intestinal microbiome in Hominids" BioRxiv.
It also holds the complete data as an R object that can be used to repeat all analyses and create all figures in the Analysis and Plots folder.
Additionaly, all cophylogeny results can be browsed here: Co-phylogeny browser.
We thank the IKMB Microbiome and NGS laboratories for excellent technical support. This study is an outcome of the Collaborative Research Center 1182, Origin and Function of Metaorganisms (https://www.metaorganism-research.com, no. SFB1182) and received infrastructure support from the DFG Excellence Cluster 2167 "Precision Medicine in Chronic Inflammation" (PMI). JFG was supported by the DFG grant “The ecology and evolution of primate phageomes” (GO 3443/1-1: Project number: 453352748) and the Deutsche Forschungsgemeinschaft (DFG) Research Group “Sociality and Health in Primates” (FOR2136; CA 1108/3-1). Research at Kokolopori was supported by the Max Planck Society and Harvard University. Research at Ozouga and Taï National Park was supported by the Max Planck Society. Research at Loango was supported by US Fish and Wildlife Service, Tusk Trust, Berggorilla Regenwald Direkthilfe, and the Max Planck Society. Research at Bwindi was supported by the Max Planck Society. The survey of the Bwindi mountain gorillas was funded by the International Gorilla Conservation Programme coalition members with supplemental funding from the Wildlife Conservation Society. We are extremely grateful to the organizations that facilitated work at these field sites and granted permission for sample collection: Bwindi—The mountain gorilla survey was conducted by the Uganda Wildlife Authority, l’Institut Congolais pour la Conservation de la Nature, the Rwanda Development Board, the International Gorilla Conservation Programme, the Max Planck Institute for Evolutionary Anthropology, Conservation Through Public Health, the Mountain Gorilla Veterinary Project, the Institute for Tropical Forest Conservation, and The Dian Fossey Gorilla Fund and was conducted in compliance with the regulations of and permission of the Uganda National Council for Science and Technology and the Uganda Wildlife Authority; Kokolopori—permission was granted through the Ministere de Recherche Scientifique et Technologie, Democratic Republic of the Congo, and work was supported by Vie Sauvage, the Bonobo Conservation Initiative; Loango—permission was granted by the Agence Nationale des Parcs Nationaux, the Centre National de la Recherche Scientifique et Technique of Gabon; Taï National Park—permission was granted by the Ministère de l’Enseignement Supérieur et de la Recherche Scientifique, the Ministère des Eaux et Fôrets in Côte d’Ivoire, and the Office Ivoirien des Parcs et Réserves, and work was supported by the Centre Suisse de Recherches Scientifiques en Côte d’Ivoire and the staff members of the Taï Chimpanzee Project. Ethical approval for work on human samples was obtained from the Local Ethics Committee Germany, Kiel (reference number A156/03), and we thank the national and local health authorities in Côte d’Ivoire and Democratic Republic of Congo as well as the according ethics commission for granting permission for this work. We thank Taylor Hermes for support in the writing of the manuscript.