Project Title: „The impact of burial environmental microbiome on biomolecular archeology and the ancient tuberculosis research”
Funding: European Regional Development Fund (ERDF), Measure 1.1.1.1 “Support for applied research”
Project No.: 1.1.1.1/16/A/101
Period: 1 March 2017 – 29 February 2020
Project costs: 648 648,24 EUR
Principle Investigator: Dr. biol. R. Ranka
Collaboration: Institute of Latvian History at the University of Latvia
Project summary:
The aim of the current project is to estimate the possible impact of the soil microbiome on the ancient DNA studies and to evaluate the presence of M. tuberculosis genome in microbiome samples of human remains from the 15th-18th centuries. Within this project innovative and multidisciplinary research is planned. To achieve the aim paleopathological and ancient infectious disease research activities will be performed by application of modern technologies for microbiome analysis of human remains and burial environment and for the detection of the presence of ancient pathogens. The implementation of the project will provide new knowledge about the environmental contamination of Medieval archeological remains with ubiquitous soil mycobacteria that will help to decipher its possible impact on ancient DNA studies. In addition, this project will attempt to detect and characterize the ancient M. tuberculosis DNA that will help to confirm and improve paleopathological diagnosis and bring the insight to the evolution processes of M. tuberculosis in Latvia.
The implementation of the project will promote the development of bioarheology and biomedicine thus contributing to the transformation of the national economy within smart specialisation areas by increasing the research and innovation capacity of scientific institutions of Latvia and by investing in human resources and infrastructure. Within this interdisciplinary collaborative project a fundamental research is planned by involving experienced scientists of Latvian Biomedical Research and Study Centre (BMC) and University of Latvia, Latvian Institute of History (LU LVI) which has a long-time experience in Molecular biology and biomedicine and Archeology sectors, respectively. The present application brings together the scientific and technical expertise and establish a collaborative network using the access to unique archaeological material. The research will be performed in a facility of Latvian Biomedical research and study centre dedicated to ancient DNA research. The effective collaborative research, the availability of unique samples and application of modern technologies in parallel to classical arheological and genome analysis methods will enable the achievment of planned results including the preparation and publication of scientific articles which, in turn, will increase the research and innovation capacity of involved scientific institutions. Together with experienced researchers, the involvement of several PhD students is planned that will contribute to the development of human resources in science in Latvia.
Information published 01.03.2017.
Progress of the project
1 March 2017 – 31 May 2017
During this period, a paleopatological study of the existing 15-18-century anthropological material has been launched and preparatory work has been carried out to carry out biomolecular analysis of these samples. The identification of the profile of micro-organisms of environmental samples using Next Generation Sequencing IonTorrent technologies. As well as the development and adaptation of bioinformatic analysis pipelines has also been initiated. An analysis of the most current scientific literature has been carried out.
Information published 31.05.2017.
Progress of the project
1 June 2017 – 31 August 2017
The first 15 – 18-century anthropological bone samples have been processed according to the appropriate methodology for obtaining ancient DNA. A characterisation of the amount of DNA obtained has been carried out, a biomolecular analysis of these samples has been initiated. The treatment of samples of the burial environment has been continued with the following identification of the profile of the micro-organisms The development and adaptation of bioinformatic analysis pipeline to project specific needs has been continued. Bioinformal analysis and processing of the resulting data has been initiated.
Information published 31.08.2017.
Progress of the project
1 September 2017 – 30 November 2017
Within this time period the paleopathological analysis of antropological remains dated by 15th-18th century has been continued. Ancient DNA isolation from several bone and tooth archeological samples has been performed followed by microbiome analysis. The bioinformatic analysis of the first obtained data has been performed. Our results showed that different 16S rRNA hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. The results were presented in the international conference.
Information published 30.11.2017.
Progress of the project
1 December 2017 – 28 February 2018
We have continued the paleopathological analysis of antropological remains dated by 15th-18th century, as well as biomolecular analysis of ancient DNA. The obtained results show that degradation of DNA molecules are closely related to the age of archeological samples. Further, the bioinformatical analysis of 16S rRNA data has been performed in order to characterize the microbiome of burial environment vs to bone samples. The obtained results have pointed out that the use of different sequencing platforms (i.e Ion Torrent and Illumina) may have additional benefit for this project.
Information published 28.02.2018.
Progress of the project
1 March 2018 – 31 May 2018
The results of the paleopathological analysis of the anthropological remains dated by 15th-18th century have revealed one new individual with skeletal changes that are probably caused by tuberculosis infection. These results have been presented in the conference. The biomolecular analysis of this individual is ongoing. The analysis of the possible presence of M. tuberculosisgenome in human remains and burial environment has been started. Mycobacterium phylum DNA has been detected in several samples. Additional analysis is necessary in order to distinguish between pathogenic M. tuberculosis and environmental Mycobacteria species.
Information published 31.05.2018.
Progress of the project
1 June 2018 – 31 August 2018
We have continued the paleopathological analysis of antropological remains, as well as biomolecular analysis of ancient DNA isolated from bone and tooth samples of the individual with skeletal changes that are probably caused by tuberculosis infection.
The bioinformatical analysis of 16S rRNA data has been started for the samples where bone-soil pair is available. Our results showed that the data clustered depending on the origin of sample, i.e. bone, teeth or soil. This result confirms that each sample has its unique microbiome print, which is not related to the soil microbiome. In addition, several possible pathogenic microorganisms were detected in archaeological remains and the analysis of the related soil samples is ongoing.
Information published: 31.08.2018.
Progress of the project
1 September 2018 – 30 November 2018
We have performed the isolation of ancient DNA from several novel individuals, as well as from the higher density bones` samples for those individuals whose previous samples failed to produce sufficient aDNA amounts. We have performed the bioinformatical analysis of 16S rRNA data for the samples where bone-soil pair is available, and the preparation of the manuscript has been started. The microbiome analysis of a tooth calculus sample of one individual has revealed the presence of Mycobacteria. Intriguing, the pathological analysis of this skeleton has showed symptoms probably caused by leprosy (M. leprae) or late tuberculosis (M. tuberculosis).
Information published: 30.11.2018.
Progress of the project
1 December 2018 – 28 February 2019
The data obtained from the bioinformatical analysis of 16S rRNA microbiome has been evaluated and the preparation of manuscript has been performed. We also have performed the enrichment processes for human DNA for several samples. This approach will enable us to obtain more information about those individuals who were tested positive for ancient pathogens. We were able to determine sex of these individuals. The analysis of mitochondrial DNA is in progress. Some additional analysis was carried out for Mycobacteria-positive samples in order to determine the species of the pathogens.
Information published: 28.02.2019.
Progress of the project
1 March 2019 – 31 May 2019
Paleopathological evaluation and biomolecular analysis of human remains from the 15th-18th centuries in Latvia has revealed an intriguing case, where severe pathological changes affected the whole skeleton of a 3-4 years old child. A macroscopic, radiographic and ancient DNA analysis was carried out, and the resulting manuscript was submitted to the journal. Further, the microbiome analysis of burial environment and archaeological samples was performed and microbial communities were identified and the microbiome patterns were compared. The resulting manuscript was prepared and submitted to the journal.
Information published 31.05.2019.
Progress of the project
June 1, 2019 – August 31, 2019
Comparison of several molecular methods for gender identification in archaeological remains using ancient DNA was performed. The results were presented during the international conference. Ancient DNA was isolated from several teeth samples and NGS sequencing by shot gun approach was performed. Also, ancient DNA was isolated from several calculus samples. Microbiome profiles were analysed and initial results were presented during the international conference. The manuscript was published in the international peer-reviewed journal (Journal of Archaeological Science).
Information published 30.08.2019.
Progress of the project
1 September 2019 – 30 November 2019
Paleopathological evaluation and biomolecular analysis of human remains from the 15th-18th centuries in Latvia has been continued with an emphasis on dental calculus samples. The data obtained from the bioinformatical analysis of microbiome has been evaluated. The analysis revealed an intriguing case of Mycobacterium leprae infection. The results were presented during international conferences.
Information published 29.11.2019.
Progress of the project
December 1, 2019 – February 29, 2020
During the last stage of the project the main focus was on the data analysis, results and preparation of manuscripts. Overall, the results were obtained from archaeological bones, teeth and calculus samples, as well as from burial environment. Paleopathological evaluation and biomolecular analysis was effectively supplemented by bioinformatical analysis using several pipelines. Three manuscripts were prepared for submission.
Information published 28.02.2020.