Deciphering function and evolution of biological systems

The main focus of this computational biology group is the analysis of microbiome data, from both the human gut and the environment. We integrate metagenomic data with associated metadata and other omics data to develop a global understanding of the interactions between bacteria and their environment and to gain insight on the development and progression of diseases. Current and past projects include:

• A global gene catalog assembled from over 13,000 metagenomic samples
• Analysis of environmental microbiomes, e.g. in the context of the TARA Oceans expedition and the TREC expedition
• Finding biomarkers for the early detection of colorectal and pancreatic cancer

In addition, we are involved in projects with other groups at EMBL, e.g. to study the interactions of proteins in the model bacterium Mycoplasma pneumoniae. For more information on our research, please also see our homepage on the main EMBL website.

Selected recent publications

• Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
  Nishijima et al., Cell, 2024

• Paternal microbiome perturbations impact offspring fitness
  Argaw-Denboba et al., Nature, 2024

• SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
  Schmidt et al., Nucleic Acids Research, 2024

• Functional and evolutionary significance of unknown genes from uncultivated taxa
  Rodríguez del Río et al., Nature, 2023

• Drivers and determinants of strain dynamics following fecal microbiota transplantation
  Schmidt et al., Nature Medicine, 2022

• A faecal microbiota signature with high specificity for pancreatic cancer
  Kartal et al., Gut, 2022

Research highlights from the past

• 2022: Towards the biogeography of prokaryotic genes by Coelho et al.

• 2021: Combinatorial, additive and dose-dependent drug-microbiome associations by Forslund et al.

• 2018: Structure and function of the global topsoil microbiome by Bahram et al.

• 2018: Extensive impact of non-antibiotic drugs on human gut bacteria by Maier et al.

• 2015: TARA Oceans special issue in Science, e.g. Structure and function of the global ocean microbiome by Sunagawa et al.

• 2015: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota by Forslund et al.

• 2013: Genomic variation landscape of the human gut microbiome by Schloissnig et al.

• 2011: Enterotypes of the human gut microbiome by Arumugam et al.

• 2010: A human gut microbial gene catalogue established by metagenomic sequencing by Qin et al.

• 2008: Drug Target Identification Using Side-Effect Similarity by Campillos et al.

• 2005: Comparative Metagenomics of Microbial Communities by Tringe et al.

• 2002: Functional organization of the yeast proteome by systematic analysis of protein complexes by Gavin et al.

• 2001: Initial sequencing and analysis of the human genome