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 2020

As partner of a JPIAMR-funded consortium, we developed a publicly available model system to study biofilm-associated antibiotic resistance (ABR) in Pseudomonas aeruginosa. Data from a genomics-driven workflow (complete genome of strain MPAO1, over 30 so far missed essential genes and important genes not covered by incomplete Illumina assemblies) was integrated with the wealth of functional genomics data available for this key pathogen and with phenotypic information of biofilms grown in a microfluidic growth chamber, allowing us to identify known and novel genes relevant for both biofilm formation and ABR.

Comparative genomics of nine Pseudomonas plant microbiome isolates allowed to identify strain-specific or accessory genes that may underlie the varying antagonistic activities observed in phenotypic assays against different life stages of the notorious potato plant pathogen Phytophthora infestans and help to elucidate potential mechanisms of action.

Finally, we devised a next-generation proteogenomics strategy that enables the community to rapidly proteotype Listeria monocytogenes strains and relate this information back to the genotype.

Find out more about the Group’s activities

Main publications 2020

  • Varadarajan AR et al.
    An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
    NPJ Biofilms Microbiomes, 10.1038/s41522-020-00154-8
  • De Vrieze M et al.
    Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight
    Front Microbiol, doi: 10.3389/fmicb.2020.00857
  • Varadarajan AR et al.
    A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships
    J Proteome Res., 10.1021/acs.jproteome.9b00842

 

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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

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