PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data
Year: 2026
Type: preprint
Abstract: Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI’s integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ∼15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI’s utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.
Authors: Louis L’Hôte, Catherine Butt, Áine Halpin, Luisa Sacristán, Valeria Mattiangeli, Pernille Bangsgaard, Lisa Yeomans, Melinda Zeder, Marjan Mashkour, Hossein Davoudi, Svend Hansen, Delphine Decruyenaere, Melissa Kennedy, Adeline Vautrin, Alisher Begmatov, Andrej B. Belinskiy, Amridin Berdimuradov, Gennadiy Bogomolov, Jacopo Bruno, Alexey Kalmykov, Jane McMahon, Jamal Mirzaakhmedov, Susan Pollock, Rocco Rante, Sabine Reinhold, Tobias Richter, Alisher Sandiboev, Eberhard Sauer, Laura Strolin, Hirofumi Teramura, Hugh Thomas, Jolijn A. M. Erven, Shigeki Nakagome, Daniel G. Bradley, Kevin G. Daly
Institutions: University College Dublin, Trinity College Dublin, University of Copenhagen, University College London, Smithsonian Institution, National Museum of Natural History, Centre National de la Recherche Scientifique, University of Tehran, Muséum national d'Histoire naturelle, Archéozoologie et Archéobotanique, Deutsches Archäologisches Institut, Zentrale, Deutsches Archäologisches Institut, Eurasien-Abteilung, "Silk Road" International University of Tourism and Cultural Heritage, The University of Sydney, The University of Western Australia, Ruhr University Bochum, Berlin-Brandenburg Academy of Sciences and Humanities, Academy of Sciences Republic of Uzbekistan, Austrian Academy of Sciences, Institute of Iranian Studies, Freie Universität Berlin, Archéologies et Sciences de l’Antiquité, Université Paris 1 Panthéon-Sorbonne, Samarkand State University named after Sharof Rashidov, University of Edinburgh, Natural History Museum of Geneva, Christian-Albrechts-Universität zu Kiel, National Museum of Ethnology
Language: English
Subfield: Archeology (arts and humanities)
Field: Arts and Humanities
Domain: Social Sciences
Open Access status: green
Funder: Smithsonian Institution
OpenAlex ID: W7204881147