Multiple roles for different microbial communities in the human gut (modified from the German newspaper Zeit covering the work of the group). Metagenomic data from thousands of individuals from all over the world are analysed.

Multiple roles for different microbial communities in the human gut (modified from the German newspaper Die Zeit, which covered the work of the group, original designed by J. Schievink). Metagenomic data from thousands of individuals from all over the world are analysed. For example, three stratifying gut microbial community types (enterotypes) have been discovered in the human population (Arumugam et al., 2011); shown are 1,000 individuals clustered by their gut microbial composition. Each individual is a dot, coloured by enterotype.

The main focus of the Bork group is to gain insights into the functioning of biological systems and their evolution, by comparative analysis and integration of complex molecular data.

Previous and current research

The group currently works on three different spatial scales, but with common underlying methodological frameworks:

  • genes, proteins and small molecules;
  • molecular and cellular networks;
  • microbial communities.

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 study of protein interaction networks (von Mering et al., Nature 2002) and comparative metagenomics (Tringe et al., Science 2005), and exploration of drug-target interactions using global human 'readouts' such as side effects (Campillos et al., Science 2008).

We currently have a number of ocean microbiome projects in the context of the Tara Oceans expedition (Bork et al., Science 2015 and references therein); however, we mainly focus on the human gut microbiome. We employ metagenomics to uncover the principles of microbial communities in humans, in both health and disease. We identified three main 'enterotypes' – or gut microbial community compositions – in developed countries (Arumugam et al., Nature 2011), and showed that each human appears to carry individual strains (Schloissnig et al., Nature 2013). With a view to practical applications, we (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), useful for diagnostics, (ii) demonstrated the implications of drugs on the gut microbiome (e.g. Forslund et al., Nature 2015) with impact for treatment and (iii) tried to reveal mechanistic aspects of faecal microbiota transplantation (Li et al., Science 2016).

Furthermore, we are engaged in tool and resource development for various purposes ranging from function annotation (SMART, eggNOG) to metagenomics profiling (Sunagawa et al., Nature Methods 2013) or gene cataloging (Li et al., Nature Biotech, 2014).

Future projects and goals

We aim to develop the basics for community-based population genetics to understand how microbial communities are transmitted or evolve, for example, by monitoring families. This requires studies of communities at the strain level (i.e. studies of genetic variations). In the future, we hope to connect microbiomics with diet and host interactions and are working together with other EMBL groups on the establishment of a drug (chemical compound)-microbe interaction network that is individual, i.e. different for each person. In this regard, we will continue to explore networks between proteins and chemicals such as lipids or carbohydrates and link them to phenotypic data such as disease status, side effects or toxicology. To foster translational research, the group is also partially associated with the Max Delbrück Center for Molecular Medicine in Berlin, the university of Würzburg and the Molecular Medicine Partnership Unit at Heidelberg University.

ERC INVESTIGATOR