Director of EMBL Heidelberg
The group currently works on three different spatial scales, but with common underlying methodological frameworks:
We usually work in new or emerging research areas and balance methodological work with biological discoveries. Past frontier research projects include participation in the Human Genome Project (Lander et al., Nature 2001), foundational work on the study of protein interaction networks (von Mering et al., Nature 2002), and comparative metagenomics (Tringe et al., Science 2005), as well as exploration of drug–target interactions using global human ‘read-outs’ such as side-effects (Campillos et al., Science 2008).
Currently, we investigate microbiomes across the globe: in oceans as part of the Tara Oceans Consortium, which uses the schooner Tara for expeditions (e.g. Bork et al., Science 2015, and references therein); in soils by global sampling (Bahram et al., Nature 2018) or specifically in the context of a coastline expedition; and in humans (mostly gut), with multiple projects studying cohorts from all over the world. We employ metagenomics to uncover the principles of microbial communities in healthy and diseased individuals. We identified three main ‘enterotypes’, or gut microbial community compositions (Arumugam et al., Nature 2011), and showed that each human appears to carry individual strains (Schloissnig et al., Nature 2013). Towards practical applications, we have: (i) identified microbial markers for a number of diseases, such as obesity (Le Chatelier et al., Nature 2013) and colon cancer (Zeller et al., Mol Sys Biol 2014; Wirbel et al., Nature Med 2019), applicable to diagnostics and (ii) demonstrated the impact of drugs on the gut microbiome (e.g. Forslund et al., Nature 2015; Maier et al., Nature 2018), with impact for individualised treatment.
Furthermore, we are engaged in tool and resource development to support our work, ranging from function annotation (SMART, EggNOG, proGenomes), via visualisation (iTOL), to metagenomics profiling and global gene cataloguing (e.g. Coelho et al., submitted, GMGC.embl.de).
We aim at a functional understanding of microbial community interactions, among microbes and with the environment. This includes the tracing of horizontal gene transfer, e.g. by mobile elements; species cross-feeding; mapping functional traits at strain level (approximated by functional modules) across phylogeny and habitats; as well as the identification of microbial early response biomarkers for man-made pollutants, such as toxins. Together with other groups at EMBL, we hope to establish interaction maps between chemical compounds and microbes, individually and in communities using advanced multi-omics approaches, with application for human (e.g. individualised diet) or planetary health (e.g. pesticide response biomarkers).