Microbiome Systems Biology

Group leader: Henrik Bjørn Nielsen

The Microbiome Systems Biology group focuses on the ecology and dynamics of the human microbiome and its interaction with the human host. In particular the role of the microbiome in human diseases has our focus. This is pursued by integration and mining of shotgun metagenomics, metatranscriptomics, metabolomics and patient data. The group is continuously developing methods for microbiome analysis. As part of Center for Biological Sequence analysis (CBS) at DTU Systems Biology, the group has access to one of the world’s largest supercomputers, Computerome, which has a comprehensive life science focused infrastructure.

The Human Gut Microbiome
The group has been involved in a series of important scientific advances in our understanding of the gut microbiome. The most notable are

  • The first gene catalogue of the human gut covering 3.3M genes
  • The enterotype concept
  • The association between microbiome richness and markers of metabolic diseases and inflammation.
  • Solving the metagenomics problem

Metagenomic Species
In 2014 the group published the first exhaustive co-abundance binning of a complex microbiome and thereby identified 741 metagenomic species including 500 novel species and about 800 bacteriophages (vira) from the human gut microbiome.

This has effectively solved the metagenomic problem as it facilitates identification and assembly of previously unknown species and mobile elements incl. plasmids and genomic islands and phages from a series of environmental samples, without cultivation or reference data.

In short, the method assumes that genes originating from a genomic entity will have similar abundance. Hence, genes that co-varied in abundance across a series of samples was put into co-abundance gene groups, whereof some were sufficiently large (> 700 genes) to be named metagenomic species.


Henrik Bjørn Nielsen
Associate Professor
DTU Bioinformatics
+45 40 57 48 64
29 MAY 2017