Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.

In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.

Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study.

Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbiteni and Cunkani-Drengeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbiteni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Cunkani-Drengeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.

A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis.

A 5,000-year-old Yersinia pestis genome (RV 2039) is reconstructed from a hunter-fisher-gatherer (5300-5050 cal BP) buried at Rinnukalns, Latvia. RV 2039 is the first in a series of ancient strains that evolved shortly after the split of Y. pestis from its antecessor Y. pseudotuberculosis ∼7,000 years ago. The genomic and phylogenetic characteristics of RV 2039 are consistent with the hypothesis that this very early Y. pestis form was most likely less transmissible and maybe even less virulent than later strains. Our data do not support the scenario of a prehistoric pneumonic plague pandemic, as suggested previously for the Neolithic decline. The geographical and temporal distribution of the few prehistoric Y. pestis cases reported so far is more in agreement with single zoonotic events.

The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.

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.

Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic.

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.

Dental disease and dietary isotopes of individuals from St Gertrude Church cemetery, Riga, Latvia.

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.

Nutrition-related health problems in a wealthy 17-18th century German community in Jelgava, Latvia.

The aim of this research is to assess the presence of stress in a high status German population from Jelgava, Latvia. The skeletal material used in this study came from a recently excavated church cemetery, with most of the burials dating to the 17-18th centuries. In total, 108 individuals (80 adults and 28 non-adults) were analysed for evidence of scurvy, rickets/osteomalacia and anaemia. The presence of scurvy and healed rickets/osteomalacia could not be confirmed in any adult individual. Among non-adults, a possible diagnosis of scurvy was considered in six individuals, and active rickets was suggested in two others. Cribra orbitalia in adult and non-adult individuals also argued for the presence of childhood stress. These results, combined with previously acquired data on linear enamel hypoplasia, indicated that children in this population suffered from nutritional deficiencies. The presence of childhood stress markers in adult individuals implies that many children survived stress episodes, possibly due to generally good access to resources, as supported by historical accounts and previous studies on stature and dental disease.