Final Report Summary - COMEMIMP (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.
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.