Release of a new version of curatedFoodMetagenomicData –cFMD v1.2.1–developed within the DOMINO project, comprises additional 835 food metagenomes from 26 datasets of recent publicly available studies, along with the 2,533 publicly available (including MASTER) food metagenomes.

Meta'omics for hacking the human microbiome

Our body harbours ~100 trillion microbes which outnumber our own cells. This microbial diversity (the "microbiome") and its functions are still largely uncharachterized but we can now try to mine it using cultivation-free sequencing-based metagenomic tools.

Main research directions

Next generation computational metagenomic tools. The potential of metagenomics is only partially expressed due to computational challenges. We are working on novel methods to profile microbiomes at increased resolution (e.g. strains) and perform large-scale comparative genomics on uncharacterized microbes.

Integrative and machine learning meta'omic approaches. We develop new machine learning tools to cope with the variability and dimensionality of microbiome profiles and provide clinically relevant signatures by integrating complementary meta'omic approaches (e.g. metatranscriptomics or metaproteomics).

Microbiome-pathogen interaction in human infections. The role of the microbiome in the acquisition and development of infections is largely unknown. By coupling longitudinal pathogen/microbiome sequencing we aim understand how the microbiome can modulate the virulence profile and antibiotic resistance of human infections.

Microbiome transmission. We study how microbes can be transmitted between different environments with specific focus on how members of the microbiome are vertically transmitted from mothers to infants at birth and horizontally between family members or individuals sharing the same environment. .