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Department of Plant and Microbial Biology

Microbial Evogenomics Lab (MiEL)

Our research interests and expertise lie in the broader field of microbial ecology. Here, we leverage approaches derived from the fields (sensu lato) of bioinformatics, genomics, and evolutionary biology to explore and characterize the so-called microbial dark matter (i.e. the bulk of microbial diversity that we are yet unable to cultivate). Although heterogeneous in topics, our work gravitates around three focal-points: I) diversity, II) function, and III) evolution.

Main research project:

Retracing the evolutionary history of mitochondria through environmental evogenomics


Microbial organisms are not only the most diverse and abundant living entities on Earth, but also the ones encompassing the largest part of life’s evolutionary radiation. Large-scale sequencing of environmental DNA showed that only a minute fraction of microbial diversity has been described, and that ‘uncultivated majority’ holds cues regarding the dawn of life and its evolution. Recent developments in sequencing technologies and bioinformatics stimulated a new ‘gold rush’ in microbial exploration by offering means to scrutinize the microbial world through circumventing the cultivation-based bottleneck (via cultivation-independent genomics). The current technology-driven rise in genomic sampling of uncultivated prokaryotic (Bacteria and Archaea) lineages altered our understanding of the ‘tree of life’ and brought to light unprecedented leads regarding our protoeukaryotic ancestry.

Although it is generally accepted that the protoeukaryotic ancestor emerged through a symbiosis between two organisms belonging to Archaea and Bacteria domains of life, little is known about the identity of the bacterial partner (which gave rise to mitochondria) and the evolutionary trajectories that it took after symbiogenesis. In our current work we tackle synergistically mitochondria’s evolutionary history (i.e. the eukaryotic bacterial reminiscence) by making use of genomic data recovered from current radiations of Eukarya and Bacteria.


  • Microbial diversity
  • Phylogenomics; deep evolutionary histories; evolution of genomic architectures
  • Genome-informed metabolic reconstructions

Founding agency:

Swiss National Science Foundation (SNSF)