COMEMIMP · Computational shotgun metagenomics to detail mother-to-infant vertical microbiome transmission and microbiome-pathogen interaction in Cystic Fibrosis
FP7 — People (Marie Curie Actions)
- Duration
- 2013-09-01 → 2017-08-31
- EU contribution
- €100,000
- Participants
- 1
- Scheme
- MC-CIG
Lines connect the coordinator with its partners.
Results in brief
Computational shotgun metagenomics to detail mother-to-infant vertical microbiome transmission and microbiome-pathogen interaction in Cystic Fibrosis
In this Marie Curie Career Integration Grant project, called CoMeMIMP, we aimed at investigating the complex ecosystem of bacteria, archaea, viruses, and micro-eukaryotes populating our body (the human microbiome) at an unprecedented level of resolution, and to use the new methodologies to unravel the dynamics of the human microbiome in human diseases and how members of the microbiome are transmitted from mothers to infants. The newly developed analytical tools are based on novel approaches at computationally analyze the output of shotgun metagenomic datasets. Shotgun metagenomics is the sequencing of the overall genetic content of a microbial community sampled in this case form the human body, and it generates several millions of short DNA fragments that need to be analyzed with advanced software and statistical tools. Supported by CoMeMIMP, my laboratory developed several tools that enabled the profiling of the members of the human microbiome with the resolution of the single strains or genomes, allowed such genomes to be put into the context of already known genomes, characterized the underinvestigated viral and Eukaryotic fraction of the community, and shed lights on the overall functions of the microbiome in the human body. The new methods have then been applied on several human diseases including the study of the lung microbiome in cystic fibrosis and the skin microbiome in psoriasis. The methods were also key in our study of the microbial transmission between mother and infants during delivery and the first days of life. Within this subproject, we identified specific microbial organisms that were vertically acquired by the infant and that successfully colonized the infant gut. At a large scale, these transmission patterns could be linked to infant health and suggest targeted probiotic interventions. The results of the project supported by CoMeMIMP have been published and are considered for publication in top-tier scientific journals and were presented in several international scientific meetings and outreach activities.
Data: CORDIS, © European Union
Project objective
The crucial biological functions of the human microbiome in health are currently being investigated with metagenomic approaches that sequence whole microbial communities from in vivo samples. The involvement of the microbiome in autoimmune diseases has been proven, and the technological transition to the second generation community-wide full-genome shotgun sequencing is potentially enabling deeper, mechanistic, and functional microbiome profiles. However, the full potential of shotgun sequencing is currently unexpressed because effective methods to analyse the produced data are missing and only few partial hypothesis-driven datasets are available. The goal of CoMeMIMP is to make a multidisciplinary breakthrough in both the analysis of shotgun metagenomic data and in the understanding of (i) the role of the human microbiome during infection and (ii) the vertical sources of the microbial and probiotic diversity in the colonizing infant gut microbiome. On the methodological aspect, I already developed the fastest and most accurate taxonomic profiling methods available, and we will fully express here the potential of metagenomic data with unprecedented strain-level resolution for all domains of life, phylogenetic/phylogenomic structure mining, and statistical predictive tools. This will have a major research impact and will provide us with invaluable additional power to address the specific hypothesis that the microbiome dictates the acquisition and severity of infections from opportunistic pathogens, and to accurately track the mother-to-infant vertical transmission of transient and resilient commensal microbiomes. We will produce and analyse metagenomic longitudinal datasets including both the microbiome and pathogen isolates in patients with cystic fibrosis, and a comprehensive map of microbial transmission from the human milk microbiome and skin to the developing infant gut microbiome paving the way to new therapeutic and probiotic intervention strategies.
Original text from CORDIS.
Participants
- UNIVERSITA DEGLI STUDI DI TRENTO · TrentoCoordinatorItaly
Links
Data: CORDIS, © European Union