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ETH Zurich

Country: Switzerland
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1,155 Projects, page 1 of 231
  • Open Access mandate for Publications
    Funder: EC Project Code: 668991
    Overall Budget: 2,499,980 EURFunder Contribution: 2,499,980 EUR
    Partners: ETH Zurich

    Understanding processes in microbial communities is a crucial task given the impact of microbial communities on environmental systems, including plants and animals. There is a rapidly increasing number of microbial communities whose collective genomes have been determined; however, it is important to uncover their collective function and to understand how community properties emerge from the properties of individual microbial types and their interactions. One habitat that has been gaining growing interest is the phyllosphere, or the aerial parts of plants, which carry out the majority of terrestrial carbon dioxide fixation. There is a urgent need to better understand the microorganisms living in the phyllosphere and an increasing awareness of the importance of indigenous microbiota and their role in microbe-microbe and host-microbe interactions for both plant growth and protection. This project aims to uncover the molecular basis shaping microbial communities in the phyllosphere in order to improve our functional understanding of microbial interaction in the context of the plant host and to unravel the principles of the formation of community pattern and function in situ. To reach these objectives, a reductionist approach will be used to generate and test new hypotheses regarding microbial interactions in phyllosphere communities. Synthetic, tractable microbial communities will be formulated and analyzed under gnotobiotic conditions. In situ community approaches will be developed and applied, while community genetics and experimental evolution will provide complementary perspectives on the community structure and function. These approaches will be mirrored by manipulating interactions on the host side through the use of plant mutants and ecotypes. Taken together, using multifaceted perspectives on microbial interactions in situ will allow unprecedented insights into the biology of bacteria living in the phyllosphere and their individual and collective function.

  • Funder: EC Project Code: 268853
    Partners: ETH Zurich
  • Funder: EC Project Code: 244947
    Partners: ETH Zurich
  • Funder: EC Project Code: 628585
    Partners: ETH Zurich
  • Open Access mandate for Publications and Research data
    Funder: EC Project Code: 897571
    Overall Budget: 191,149 EURFunder Contribution: 191,149 EUR
    Partners: ETH Zurich

    The human gut is the habitat for trillions of microbial cells living in synergy with each other and with the host. While metagenomic studies of the gut microbiome have provided a wealth of DNA sequence data, functional studies of gut bacteria remain challenging. To study the gut microbiome from a functional perspective, understanding host-microbe and microbe-microbe interactions is key. These contacts are often established by specialized molecules termed secondary metabolites or natural products (NPs). The machinery required to synthesize these metabolites is encoded in bacterial genomes by biosynthetic gene clusters (BCGs). Remarkably, even though 14,000 BGCs were identified in the human microbiota, very little is known about the identities and functions of their products. To address that, we will focus on NPs of the ribosomally synthesized and post-translationally modified peptide (RiPP) family, the second most abundant NP class in the human gut. The Piel group recently discovered unprecedented RiPPs with altered peptide backbones, challenging the paradigm that ribosomal synthesis is limited to the L-alpha-amino acid topology. These modifications include the excision of a tyramine moiety from a tyrosine-glycine motif, which introduces an alpha-keto-beta-amino acid in the peptide precursor backbone; and the epimerization of amino acids from L- to D-configuration. Enzymes homologous to these backbone-modifying catalysts and associated with RiPP gene clusters have been found bioinformatically in a wide variety of bacterial genomes, including gut microbiome representatives. The pervasiveness of these BGCs in microbiome bacteria suggests a function for these metabolites and possible therapeutic applications. This proposal aims to identify the products of these gene clusters in representatives of the most abundant phyla in the gut microbiome. In addition, we will examine the functions of the discovered metabolites utilizing bioactivity assays and chemical proteomics.