What we do

We focus on the bioinformatic analysis and integration of state-of-the-art functional genomics data, which we obtain through close collaboration with experimental biologists. These datasets include genome sequences, gene and protein expression, metabolomics and Tn-seq data.
One focus is to exploit the unique advantages of proteomics data, including strategies to identify all proteins encoded in a genome (proteogenomics) including small proteins, which are often missed. Additional focus areas are studying the role of microbiomes – e.g. for plant protection – by applying metagenomic, comparative genomic and transcriptomic approaches and integration of the resulting datasets, and to understand antibiotics resistance development.

Highlights 2019

Using long read sequencing data able to span intragenomic as well as intergenomic repeats, we achieved the de novo assembly of the complete genomes of all dominant bacterial species and phages directly from a low complex metagenome sample, the starter cultures in cheese production. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages.

We applied our integrative proteogenomics strategy to identify missed prokaryotic protein-coding genes on Bradyrhizobium diazoefficiens USDA 110. Based on the re-sequenced genome of the lab strain we could identify both proteogenomic novelties as well as proteins regulated at the post-transcriptional level (similar to FixK). Integrated proteogenomics databases for several B. diazoefficiens strains are available at the public web server (iPtgxDBs).

Finally, we contributed to the elucidation of the mechanism of action enabling Metschnikowia pulcherrimia to exert biocontrol activity versus several plant pathogenic fungi.

Find out more about the Group’s activities

Main publications 2019

  • Somerville V et al.
    Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
    BMC Microbiol, doi: 10.1186/s12866-019-1500-0
  • Fernandez N et al.
    An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens
    Front Microbiol, doi: 10.3389/fmicb.2019.00924
  • Gore-Llyod D et al.
    Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima
    Mol Microbiol, doi: 10.1111/mmi.14272

Home

 

Members

Zurich university waedenswil

Christian Ahrens
Bioinformatics and Proteogenomics Group
Agroscope, Wädenswil
Group Webpage

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

Tags