What we do

We focus on the bioinformatic analysis and integration of state-of-the-art functional genomics data that we obtain through close collaboration with experimental biologists (genome sequences, gene and protein expression, metabolomics, Tn-seq data).

Complete, de novo assembled genomes are an optimal basis for functional genomics studies. We aim to identify all proteins encoded in a genome by proteogenomics, including small proteins that are often missed (e.g., antimicrobial peptides), thereby improving genome annotations. We also study the role of microbiome isolates – e.g. for plant protection – by applying metagenomic, comparative genomic and transcriptomic approaches. Finally, we aim to understand biofilm-mediated antibiotic resistance.

Highlights 2021

Using our integrative proteogenomics strategy, we identified novel small protein-coding genes in a model system of the human gut microbiome consisting of eight bacterial species, thereby extending our approach from single isolates to low complex communities. Notably, the novel genes included examples of anti-microbial peptide coding genes whose products could specifically inhibit the growth of other consortium members and a novel gene as part of an operon predicted to play a role in community metabolism. We also contributed our proteogenomics expertise to identify novel protein-coding genes in Staphylococcus aureus and published a best practices article on how to identify small proteins by mass spectrometry.

Moreover, we continued to describe microbiomes and particularly relevant taxa, e.g. involved in biocontrol. The de novo assembly of complete genomes of the most potent individual isolates, represent an ideal basis for functional genomics. Integrating transcriptomics and proteomics data helped to identify a limited subset of genes/proteins potentially relevant for biocontrol, i.e., candidates for further detailed functional analysis.

Main publications 2021

  • Petruschke H et al.
    Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
    Microbiomes, 10.1186/s40168-020-00981-z
  • Fuchs S et al.
    Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach
    PLoS Genet, 10.1371/journal.pgen.1009585
  • Rueda-Mejia M P et al.
    Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes
    Microb Cell, 10.15698/mic2021.08.757





Zurich university waedenswil

Christian Ahrens
Bioinformatics and Proteogenomics Group
Agroscope, Wädenswil

Domain(s) of activity:

  • Proteins and proteomes
  • Comparative genomics
  • Data mining
  • Drug resistance
  • Functional genomics
  • Metagenomics
  • Microbiology
  • Next generation sequencing
  • Proteomics
  • Software engineering
  • Transcriptomics

Domain(s) of application:

  • Agriculture
  • Basic research