Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth-eighteenth century) that started with the Black Death (1,347-1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe. Yersinia pestis (Y. pestis) is the causative agent of plague that evolved from a relatively benign pathogen-Yersinia pseudotuberculosis-thousands of years ago 1-4. Whilst plague is a zoonotic disease with rodents being the primary hosts of the pathogen 5-7 , it has also afflicted humans for at least 5,000 years 1. In the last two millennia, Y. pestis was responsible for three major epidemics, of which the second was the most infamous. This pandemic began with the Black Death in the fourteenth century (1,346-1,353). It is thought to have originated in Asia from where it quickly spread to and across the European continent killing approximately 30-50% of the population within a few years 8,9. The second pandemic persisted for over 400 years 10 causing, among others, the Great Plague of London (1,665-1,666) and Marseille (1,720-1,722) 11. In contrast to western Europe, the first major outbreaks of plague in the northeastern part of the continent took place mainly in the post-Black Death period (after 1,353),

Highlightsd Yersinia pestis is discovered in a 5,000-year-old huntergatherer from Latvia d Y. pestis emerged 7,000 years ago at the beginning of the Neolithic d The infected individual might represent a case of septicemic plague due to zoonosis

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

This research explores oral health indicators and stable carbon and nitrogen isotope data to explore diet, and differences in diet, between people buried in the four different contexts of the St Gertrude Church cemetery (15th– 17th centuries AD): the general cemetery, two mass graves, and a collective mass burial pit within the general cemetery. The main aim is to assess whether people buried in the mass graves were rural immigrants, or if they were more likely to be the victims of plague (or another epidemic) who lived in Riga and its suburbs. The data produced (from dental disease assessments and isotope analyses) were compared within, as well as between, the contexts. Most differences emerged when comparing the prevalence rates of dental diseases and other oral health indicators in males and females between the contexts, while isotope analysis revealed more individual, rather than context-specific, differences. The data suggested that the populations buried in the mass graves were different from those buried in the general cemetery, and support the theory that rural immigrants were buried in both mass graves. Significant differences were observed in some aspects of the data between the mass graves, however, possibly indicating that the people buried in them do not represent the same community.

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