Velsko, Irina M.Fagernäs, ZandraTromp, MonicaBedford, StuartBuckley, Hallie R.Clark, GeoffreyDudgeon, JohnFlexner, JamesGalipaud, Jean ChristopheKinaston, RebeccaLewis, Cecil M.Matisoo-Smith, ElizabethNägele, KathrinOzga, Andrew T.Posth, CosimoRohrlach, Adam B.Shing, RichardSimanjuntak, TrumanSpriggs, MatthewTamarii, AnatauariiValentin, FrédériqueWillie, EdsonWarinner, Christina2025-05-232025-05-232041-1723PubMed:39582065ORCID:/0000-0002-9055-655X/work/184100435http://www.scopus.com/inward/record.url?scp=85210091986&partnerID=8YFLogxKhttps://hdl.handle.net/1885/733752765The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.We thank M. Abong of the Vanuatu Cultural Centre (VCC) for assistance during calculus sampling. Sampling of the Teouma dental calculus was done through a research agreement between M.T. and the Vanuatu National Cultural Council. The Teouma Archaeological Project is a joint initiative of the Vanuatu National Museum and the Australian National University (ANU), directed by M.S. and S.B. and at different times R. Regenvanu and M. Abong, both former Directors of the VCC. Funding for the project was provided by the Australian Research Council (DP 0556874 to S.B. and M.S.), the National Geographic Society (SRC 8038\u201306 to M.S.), the Pacific Biological Foundation (to M.S.), the Department of Archaeology and Natural History and School of Archaeology and Anthropology at the ANU (S.B. and M.S.), the Snowy Mountains Engineering Corporation Foundation (S.B. and M.S.) and Brian Powell (to S.B. and M.S.). The laboratory research and travel for excavation of the skeletal remains were funded by The Royal Society of New Zealand Marsden Fund (UOO0407 and 09-UOO-106 to H.R.B.) and a University of Otago Research Grant (to H.R.B). The support of the leaseholder M. R. Monvoisin and family is acknowledged, as is the support and assistance of the traditional landowners and population of Eratap Village. Detailed acknowledgement by the authors of the Vanuatu studies (S.B., H.R.B., J.F., R.S., M.S., E.W., and F.V.) are given in the published site reports for each location, and were supported by the Australian Research Council DP160103578 (to J.F., S.B., and F.V.). The excavation of the Pain Haka site in 2012 was funded by a grant from the Research Institute for Development (UMR Paloc to G.C.) and by additional funding from the French Embassy in Indonesia (to G.C. and T.S.), as well as a University of Otago Research Grant awarded to H.R.B. for the excavation and analysis of the human skeletal remains. Additional funding was provided by an Australian Research Council Discovery Grant (DP170100732 and DP200102872 to G.C.). Genetic data generation and analysis was supported by the Werner Siemens Stiftung (\u201CPaleobiotechnology\u201D to C.W.) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany\u2019s Excellence Strategy (EXC 2051, Project-ID 390713860 to C.W.). The Otago research presented here was funded by a University of Otago Doctoral Scholarship (to M.T.), a Royal Society of New Zealand Skinner Fund grant (to M.T.) and an Otago Centre for Electron Microscopy Student Research Award (to M.T.). We thank Alexander H\u00FCbner for discussions on strain analyses. The skeletal remains from the Sigatoka Dunes site on the island of Viti Levu in Fiji were sampled in 2015 from prior excavations curated at the Fiji Museum, Suva, Fiji. The original excavations were conducted under the Sigatoka Salvage Archaeological Project by Simon Best in 1987 and 1988. Sampling of skeletal remains was approved by the Fiji Ministry of Education and the Immigration Department and by the Fiji Museum, and sampling was assisted by museum staff Sepeti Matararaba, Jone Balenaivalu, Elia Nakoro, Sakiusa Kataiwi, and Jotami Naqeletia. Funding for this research was provided by the Nation Science Foundation of the United States, Award # SBS 1216310.enPublisher Copyright: © The Author(s) 2024.202410.1038/s41467-024-53920-z85210091986