What we do

We are interested in studying ecological and evolutionary factors that determine the structure, function and diversity of microbial communities – with a focus on the ocean ecosystem and the gastrointestinal tract of animals and humans. To this end, we develop and combine bioinformatic and experimental approaches to integrate quantitative ‘meta-omics’ readouts with contextual information, with the goal to better understand and predict the role of environmental microorganisms and the underlying mechanisms of host-microbial homeostasis.

Find out about the Group’s activities

Publications 2021

  • Zünd M et al.
    High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-​to-host ratios in gut microbial strains
    Microbiome, 10.1186/s40168-021-01033-w
  • Salazar G et al.
    mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes
    Bioinformatics, 10.1093/bioinformatics/btab465
  • Ruscheweyh HJ et al.
    mOTUs: profiling taxonomic composition, transcriptional activity and strain populations of microbial communities
    Curr Protoc, 10.1002/cpz1.218


eth zurich

Shinichi Sunagawa
Microbiome Research Group
ETH Zurich
Group webpage


Domain(s) of activity:

  • Genes and genomes
  • Systems biology
  • Genome reconstruction
  • Metagenomics
  • Microbiology
  • Next generation sequencing
  • Software engineering

Domain(s) of application:

  • Basic research