Release of MetaPhlAn 4.1, which, among other updates, allows virome profiling through the newly developed MetaPhlAn 4 viral module. Have a look at the preprint for details.

Meta'omics for hacking the human microbiome

  • "Taxonomic, functional, and strain-level profiling with bioBakery 3" (eLife, 2021)
  • "Benchmarking viromes enrichment" (Nat. Biotechnology 2019)
  • "A catalog of 154,000 genomes and 5,000 SGBs" (Cell 2019)
  • "Vertical microbiome transmission" (Cell Host & Microbe 2018)
  • The laboratory and our little friends
  • Microbiome signatures (Pasolli et al, PLOS ComBio, 2016)
  • Strain diversity on the skin (Tett et al, 2016)

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.

We employ experimental meta'omic tools and novel computational approaches to study the diversity of the microbiome and its role in human dysbiosis and infections. Our projects bring together computer scientists, microbiologists, statisticians, and clinicians.

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. .

Our Keywords (from our papers)

Wordle: CibioCM