Background Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease’s complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. Results Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae’s genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. Conclusions Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease’s global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy’s global history and can contribute to current models of M. leprae’s worldwide dissemination, including interspecies transmissions.

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Advances in geochemical and physical anthropological studies have provided new tools to reconstruct ancient lifestyles, especially of those minorities not commonly mentioned in historical texts. In comparison to males, little is known about everyday life in female monastic communities, and how it has changed over time. In this paper, we present a paleodietary (δ 13 C and δ 15 N in bone collagen) study of human (n = 58) and animal (n = 13) remains recovered from the former Convent of Santa Catalina de Siena in Belmonte (Cuenca, central Spain). Two funerary areas used by Dominican nuns were sampled: one dated to the sixteenth (n = 34) and the seventeenth (n = 15) centuries, and the other dated in the nineteenth and twentieth (n = 9) centuries. The isotopic values for sheep (n = 7) suggest the animals consumed at the convent came from diverse ecosystems or were raised under a range of management strategies. The human samples reflect a terrestrial diet, and those from the nineteenth to twentieth century, in some cases, reveal the presence of C 4 plants (millet, corn or sugar cane). Due to their religious practice, the consumption of terrestrial animal protein was restricted, and although they were allowed to eat fish, the isotopic signatures show little evidence of this. The individuals from the sixteenth and seventeenth century show a continuous shift in δ 15 N (9.7-12.7‰), with few significant differences in relation to the period, age, or pathologies (osteoporosis, periostitis, and brucellosis). The nineteenth-to twentieth-century samples can be divided into two groups: (a) one that fits the trend of previous centuries, albeit with a higher δ 15 N, possibly related to extensive access to animal protein; and (b) a second group with elevated δ 13 C values (up to − 15.7‰). Different customs in the assumed homogeneous monastic life are discussed as possible sources of isotopic variation, including access to luxury products such as animal protein or sugar, or the practice of periods of food abstinence, which were especially popular with these communities, according to historical records.

While there have been numerous studies investigating intestinal parasitic infection in the Roman period, much of this work has been focused in northern Europe, with major gaps in the eastern empire. In order to further elucidate regional patterns in parasitic infection in the Roman empire, we looked for evidence for parasites in sites from Anatolia and the Balkans. Sediment samples from drains as well as coprolites were studied to find evidence for intestinal parasites in the Roman cities of Viminacium (Serbia) and Sardis (Turkey), and results were combined with previous work in these regions. Each sample was tested for preserved helminth (worm) eggs using microscopy and for intestinal protozoa that cause diarrhea, using enzyme-linked immunosorbent assay (ELISA). Our analysis revealed a predominance of species spread by the contamination of food and water by human feces, namely roundworm and whipworm. The identification of these parasites (which are linked to sanitation and hygiene) in Roman cities in Anatolia and the Balkans is contrasted with the range of zoonotic species found elsewhere in the empire. It appears that variations in cooking practices, diet, urbanization, and climate throughout the empire may have contributed to differences in gastrointestinal diseases in different regions. 1 1 We would like to thank Techlab © for donation of the ELISA kits used in this study. We would also like to thank the excavation teams at Sardis and Viminacium who made collection of these samples possible.

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