Identification of microbial pathogens in Neolithic Scandinavian humans

www.nature.com/scientificreports OPEN Identification of microbial pathogens in Neolithic Scandinavian humans Nora Bergfeldt 1,2,3*, Emrah Kırdök 4, Nikolay Oskolkov 5, Claudio Mirabello 6, Per Unneberg 7, Helena Malmström 8, Magdalena Fraser 8, Federico Sanchez‑Quinto 8, Roger Jorgensen 9, Birgitte Skar 10, Kerstin Lidén 11, Mattias Jakobsson 8, Jan Storå 11 & Anders Götherström 1,11 With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts. During the Neolithic transition, the human lifestyle and subsistence shifted from hunting and gathering to an agricultural lifestyle. In Europe, the transition appears to have been largely associated with mobility, seen in many recent archaeogenetic studies as a marked process of geneflow from A natolia1,2. In Scandinavia, the Neolithic period started with the appearance of the cultural complex called the Funnel Beaker culture (FBC) c. 6000 years before present (BP)3,4. The FBC cultural complex, often with a major ancestry component deriving from Anatolian Neolithic f armers1,5–7, persisted until c. 4800 BP and was succeeded by the Battle Axe culture (BAC, c. 4800–4300 BP)8. However, an important hunter-gatherer cultural complex, the Pitted Ware culture (PWC), existed in parallel (c. 5400–4400 BP) with the above agricultural complexes, mainly along the coast of southern Scandinavia9. Individuals from a PWC context have been shown to share a large portion of genetic ancestry with chronologically older European Mesolithic hunter-gatherers10, and although Neolithic farmer and hunter-gatherer groups were genetically distinct, gene flow from PWC to FBC individuals has been detected5. Individuals from a BAC context seem to share most genetic ancestry with other groups on the European continent, especially the Corded Ware culture (CWC)11. However, while there is ample archaeological evidence that there were both social and cultural interactions between individuals from the PWC and BAC complexes in Scandinavia, so far there is no genetic evidence for interactions between the groups, as seen e.g. on G otland12. Apart from the change in subsistence strategies, the Neolithic transition entailed changes in d emography13. Larger and more dense populations could potentially have provided environments where diseases could spread more easily14, increasing both the pathogen load and dispersal modes. Besides a higher population density, the migration of human populations itself, during this time, could also have facilitated the dispersal of human microbiomes. Further, it has been suggested that keeping domesticated livestock can promote zoonotic transmissions of diseases15. 1 Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden. 2Department of Zoology, Stockholm University, Stockholm, Sweden. 3Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden. 4Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey. 5Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden. 6Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden. 7Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden. 8Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden. 9Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway. 10Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway. 11Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden. *email: Scientific Reports | (2024) 14:5630 | https://doi.org/10.1038/s41598-024-56096-0 1 Vol.:(0123456789) www.nature.com/scientificreports/ Dispersal of microbes can now be approached using archaeogenetic methods and may provide important insights into living conditions and health in the past. By the introduction of high-throughput sequencing, specific diseases such as plague and paratyphoid fever have been possible to study in prehistoric/historic populations16–19. Moreover, metagenomic studies have made it possible to detect changes in the human microbiota over time and how these changes affected human prehistoric populations. For example, early Mesolithic hunter-gatherers in present-day Poland exhibited fewer caries- and periodontal disease-associated microbe taxa than Neolithic farming groups in present-day G ermany20. This is in accordance with observations on the incidence of actual lesions in the dental record of hunter-gatherer and farmer groups. Further, studies based on coprolites on more modern human populations, industrialized versus non-industrialized, have shown differences in gut m icrobiome21. Here, we performed a metagenomic analysis of aDNA extracted from teeth of 38 Stone Age individuals recovered from eleven sites in Scandinavia. The samples came from different cultural contexts: Mesolithic huntergatherers, named here (SHG); Neolithic hunter-gatherers from the Pitted Ware culture (PWC); two Neolithic cultures (FBC and BAC); and two chronologically younger samples from Late Neolithic Farmers (Ans004 and Ans010) from a d olmen22, named here (LNF). A sample from Steigen in Norway has been dated to the Neolithic period, but genetic data and isotope analysis indicates close affinity to Mesolithic hunter-gatherers 6 and the sample is thus treated as a Mesolithic hunter-gatherer in this study. Our purpose was to investigate the microbial content of these skeletal samples to gain understanding of their health and living conditions. We also explored whether we could find microbes in more than one cultural context, which could indicate possible transmissions and thus contacts between Neolithic hunter-gatherer (PWC) and other Neolithic populations (FBC). Samples We analyzed shotgun-sequenced DNA from 38 individuals for microbial species. The (...truncated)