Funding: European Regional Development Fund (ERDF) “On Implementation of Activity 1.1.1.2 “Post-doctoral Research Aid” of the Specific Aid Objective 1.1.1 “To increase the research and innovative capacity of scientific institutions of Latvia and the ability to attract external financing, investing in human resources and infrastructure” of the Operational Programme “Growth and Employment”
Project Title: Association of human intestinal and blood microbiome composition with general state of health and mortality within population of Latvia
Project No.: 1.1.1.2/VIAA/3/19/460
Period: 36 months (1 March 2020 – 28 February 2023)
Project costs: 133 806.00 EUR
Project implementer: Dr. biol. Dāvids Fridmanis
From microbiological point of view intestinal tract is very dynamic ecosystem, which is believed to be linked to blood microbiome. Latest discoveries revealed that alterations of microbial population in both sites are associated with various diseases. However there were only few studies that focused on their associations with general health status and there are no reports on association with mortality. The most probable reason to that is related to lengthiness of such studies, because years are needed for sample acquisition. Here in Latvia the collection of samples was started in 2013 and currently there are samples and detailed information from more than 7000 residents and 31 of these have died in non-violent death. Within the scope of this industrial study I shall perform intestinal metagenome and blood 16SrRNA sequencing on samples from 217 individuals. Our study group shall encompass six sample sets: control, deceased, autoimmune, intestinal cancer, cardiovascular and viral hepatitis. As the result of successful project implementation I shall uncover the elements of microbiome that are common to all or groups of case sets. The elements that are associated with decrease in survival could also be uncovered. These results might be applicable in development of various screening programs.
Information published 02.03.2020.
Project progress
1 March 2020 – 31 May 2020
During this project period, work was started on the preparation of the project implementation related application for acquisition of medical ethics commission approval, these activities included assessment of available samples and available clinical and phenotypic information within the partner’s collection, these activities also included considerations regarding which of the commissions (RAKUS or CMEK) the application should be sent. In parallel to these activities selection of samples and an in-depth study of the literature on the most appropriate blood microbiome isolation methods and the necessary the isolation process controls was performed .
Information published 31.05.2020.
Project progress
1 June 2020 – 31 August 2020
During this project period, the work on the preparation of the application of the project medical ethics commission was continued, within the framework of which the potential samples of the partner’s collection were selected, the available clinical and phenotypic information was summarized. It was decided that the application will be submitted to CMEK. In parallel with these activities, a blood microbiome isolation method was developed, and all the materials necessary for the first phase of the study, fecal analysis, were procured.
Information published 31.08.2020.
Project progress
1 September 2020 – 30 November 2020
During this project period, the work on the preparation of the application of the project medical ethics commission was continued, within the framework of which the potential samples of the partner’s collection were selected, the available clinical and phenotypic information was summarized. It was decided that the application will be submitted to CMEK. In parallel with these activities, a blood microbiome isolation method was developed, and all the materials necessary for the first phase of the study, fecal analysis, were procured.
Information published 30.11.2020.
Project progress
1 December 2020 – 28 February 2021
During this project period, the work on the preparation of the application of the project medical ethics commission was continued, also the first experiments on blood microbiome extraction were conducted. In parallel to these activities, processing of samples and preparation of sequencing libraries was continued.
Information published 26.02.2021.
Project progress
1 March 2021 – 31 May 2021
During this project period, the work on the preparation of the application of the project medical ethics commission was continued and the research protocol was developed. In parallel to these activities, the first fecal samples were processed and sequencing libraries were prepared.
Information published 31.05.2021.
Project progress
1 June 2021 – 31 August 2021
During this project period, the work on the preparation of the project’s application for the acquisition of medical ethics permit was completed and submitted to the Central Medical Ethics Committee. On the practical side, the processing of fecal samples, sequencing library sequencing and sequencing was continued. At this moment, genetic material was obtained and sequencing libraries were prepared from 183 fecal samples, while sequencing was performed on 11 samples. Work on the isolation of the blood microbiome from patient samples and the analysis of sequencing data will begin after acquisition of ethics committee permit.
Information published 31.08.2021.
Project progress
1 September 2021 – 30 November 2021
During this project period, a decision letter was received from the Central Medical Ethics Commission, which stated support for the implementation of the study. However it also stated request to supplement study protocol with a statement that the study would be conducted in accordance with the Taipei Declaration. In the weeks following this event, the study protocol was amended accordingly and, as required, an updated version was sent to the Central Medical Ethics Commission for information. On the practical side, work continued on the processing of faecal samples, the preparation of sequencing libraries and their sequencing. At this time, genetic material was obtained and sequencing libraries have been prepared from 186 faecal samples, while sequencing was performed on 31 samples. Following the positive response from the Ethics Commission, work was started on the extraction of blood microbial DNA from the first patient samples and the development of a workflow for the analysis of faecal sequencing data.
Information published 30.11.2021.
Project progress
1 December 2021 – 28 February 2021
During this project period, sequencing of all previously prepared sequencing libraries was performed. The obtained data of all 186 samples met the requirements and their analysis was started employing the developed data analysis pipeleine. In parallel with sequencing related activities, the work was continued on the isolation of microbial DNA from blood, Thus far 12 samples have been successfully processed.
Information published 28.02.2022.
Progress of the project
1 March 2022 – 31 May 2022
During this project period the analysis of whole metagenome sequencing data and extraction of blood microbial DNA was continued. In addition work was carried out on preparation of the first blood microbial DNA sequencing libraries. Thus far, extraction has been performed for 186 blood samples and library preparation has been successfully performed for 16 samples.
Information published 31.05.2022.
Progress of the project
1 June 2022 – 31 August 2022
At the moment, work is being continued on the analysis of the whole metagenome sequencing data analysis. Also the library preparation and their sequencing has been completed for all obtained blood microbial DNA samples and the analysis of the obtained data has been started.
Information published 31.08.2022.
Project progress
1 September 2022 – 30 November 2022
During this project period, the work on the extraction of genetic material from biological samples was completed, and the total number of processed samples reached 217 fecal and 217 blood samples. Also the preparation and sequencing of all remaining fecal and blood sample sequencing libraries has been completed. In parallel with the practical works, the work was continued on the analysis of the whole metagenome sequencing data and the development of the blood microbiome sequencing data analysis workflow. As of last, the quantification of the microbial DNA in the blood samples was also started.
Information published 30.11.2022.
Project progress
1 December 2022 – 28 February 2023
During this project period, Mobility-related activities were implemented. Within their framework, a virtual visit was made to the European molecular biology laboratory – the European Institute of Bioinformatics. During the visit, sequencing data analysis and various statistical analysis tools and methods were learned. During this project period, the work on the isolation of genetic material from biological samples was completed, and the total number of samples processed reached 217 fecal and 217 blood samples, however, the isolation of some samples was not successful and some could not be replaced. The preparation and sequencing of all remaining fecal and blood sample sequencing libraries was also completed. In parallel with the practical works, the work on the analysis of the whole metagenome sequencing data and the development of the blood microbiome sequencing data analysis workflow were carried out. In parallel, the quantification of microbial DNA in the blood sample was also performed.
Information published 28.02.2023.