DiMeTrack · Assembly-based discovery of uncharacterized human microbiome members and their tracking across individuals and time
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2016-10-01 → 2018-12-01
- EU contribution
- €180,277
- Participants
- 1
- Scheme
- MSCA-IF-EF-RI
Lines connect the coordinator with its partners.
Results in brief
Assembly-based discovery of uncharacterized human microbiomemembers and their tracking across individuals and time
The microbiome - the large set of micro-organisms that live and interact with the environment in which they live - has received a growing interest in the last few years due to its fundamental role in the human health, in the environment, and in different natural ecosystems. Although microbial communities have been investigated for decades, significant advances have been obtained through the introduction of high-throughput next-generation DNA sequencing technologies, and in particular thanks to shotgun metagenomics. Despite extensive recent studies using shotgun approaches, most characterization of these ecosystems has been focused on microbes that are easily cultivable and has suggested the presence of a large fraction of still unexplored diversity. New approaches and experimental analysis that are scalable to large cohorts are necessary in order to increase our knowledge of the microbiome from metagenomic approaches. The MSCA DiMeTrack (leaded by Dr. Edoardo Pasolli and supervised by Prof. Nicola Segata at University of Trento, Italy) aimed to expose and characterize previously unknown members of the human microbiome. Through the application of existing and newly developed methodologies, we analysed around 10,000 metagenomes acquired from public repositories or newly generated in the host laboratory. We reconstructed and characterized several thousands of genomes and identified thousands of new species without reference genomes in public databases. The genomes were analysed in multiple projects in order to answer to different biological relevant problems. All the data and software generated were made freely available to the community, therefore representing an important resource for future studies on the human microbiome.
Data: CORDIS, © European Union
Project objective
In this proposal we aim to expose and characterize members of the human-associated microbial dark matter and exploit the novel information to dramatically enhance the resolution of metagenomic profiling and develop accurate predictive/diagnostic tools.As a first step we will discover currently uncharacterized human microbiome members from metagenomic data through novel application of assembly-based approaches on a large compendium of newly generated and available shotgun metagenomes (Aim 1). The new identified genomes will be phylogenetically and taxonomically characterized and investigated to track strain-level individual and temporal genetic variability (Aim 2). The new genomes will be then used to develop a next generation host condition prediction approach through a genome-level machine learning tool (Aim 3).The three main objectives of the proposal are functional to the characterization of microbial dark matter from human microbiome and its use for strain-level microbiology tasks and metagenomic prediction/association tools. DiMeTrack focuses specifically on shotgun metagenomics and tracking across time and individual on many samples from publicly available databases and generated at the host laboratory. By discovering previously uncharacterized microorganisms and unravelling their roles in specific biological phenomena (e.g., mother-to-neonate transmission) and association with disease states, we fulfil the Horizon 2020 policies in supporting research and innovation that improve our understanding of the causes and mechanisms underlying healthy and diseased people and improve our ability to monitor and detect diseases.The profile and the future research plan of the applicant fits well with these research areas. In addition, after working in United States for a few years, he wants to be reintegrated in a research position in EU.
Original text from CORDIS.
Participants
- UNIVERSITA DEGLI STUDI DI TRENTO · TrentoCoordinatorItaly
Links
Data: CORDIS, © European Union