Phyllosphere microbiome


Plants do not exist as sterile organisms but are populated by microorganisms both below (rhizosphere) and above the ground (phyllosphere). We are interested in a systems-level understanding of the phyllosphere with the aim to identify organizing principles of bacterial community members. We developed a cultivation-independent metaproteogenomic approach and applied it to phyllosphere communities of different host plants in planta in order to get an unbiased view on the overall bacterial community composition and in particular to identify abundant proteins as a proxy for important protein function of community members in the habitat.

Such analyses are paralleled by work using synthetic microbial communities colonizing Arabidopsis thaliana. We are testing indigenous commensal bacteria and their interaction with the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on the model plant and investigate underlying mechanisms of plant protection.


Recent Publications

  • A general non-self response as part of plant immunity
    Maier BA, Kiefer P, Field CM, Hemmerle L, Bortfeld-Miller M, Emmenegger B, Schäfer M, Pfeilmeier S, Sunagawa S, Vogel CM, and Vorholt JA.
    Nat Plants 7: 696–705 (2021). doi: 10.1038/s41477-021-00913-1.
  • The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves.
    Pfeilmeier S, Petti GC, Bortfeld-Miller M, Daniel B, Field CM, Sunagawa S, and Vorholt JA.
    Nat Microbiol (2021). doi: 10.1038/s41564-021-00929-5.
  • Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection
    Ledermann, Raphael; Emmenegger, Barbara; Couzigou, Jean-Malo; Zamboni, Nicola; Kiefer, Patrick; et al.
    Mbio  10.1128/mBio.00390-21 Published: MAR-APR 2021
  • Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
    Keller, Philipp; Noor, Elad; Meyer, Fabian; Reiter, Michael A.; Anastassov, Stanislav; Kiefer, Patrick; Vorholt, Julia A
    Nature Communications   DOI: 10.1038/s41467-020-19235-5  OCT 26 2020
  • Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus
    Shyp, Viktoriya; Dubey, Badri Nath; Bohm, Raphael; Hartl, Johannes; Nesper, Jutta; Vorholt, Julia A; Hiller, Sebastian; Schirmer, Tilman; Jenal, Urs
    Nature Microbiology  DOI: 10.1038/s41564-020-00809-4  NOV 2020
  • Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins
    Snelders, Nick C.; Rovenich, Hanna; Petti, Gabriella C.; Rocafort, Mercedes; van den Berg, Grardy C. M.; et al.
    Nature Plants  DOI: 10.1038/s41477-020-00799-5  Published: NOV 2020
  • Import of Aspartate and Malate by DcuABC Drives H-2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice
    Nguyen, Bidong D.; Cuenca, Miguelangel, V; Hartl, Johannes; Guel, Ersin; Bauer, Rebekka; et al.
    Cell Host & Microbe  DOI: 10.1016/j.chom.2020.04.013  Published: JUN 10 2020
  • ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
    Millard, Pierre; Schmitt, Uwe; Kiefer, Patrick; Vorholt, Julia A.; Heux, Stephanie; et al.
    Plos Computational Biology APR 2020
  • Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum
    Wolf, Natalie; Bussmann, Michael; Koch-Koerfges, Abigail; Katcharava, Nino; Schulte, Julia; et al.
    Frontiers In Microbiology 11 Article Number: 87 DOI: 10.3389/fmicb.2020.00087    FEB 11 2020
  • Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species
    Massoni, Julien; Bortfeld-Miller, Miriam; Jardillier, Ludwig; Salazar, Guillem; Sunagawa, Shinichi; Vorholt JA
    Isme Journal,  DOI: 10.1038/s41396-019-0531-8   OCT 2019
  • Escherichia coli in Auto(trophic) Mode
    Erb, Tobias J.; Keller, Philipp; Vorholt, Julia A.
    Cell,  DOI: 10.1016/j.cell.2019.10.040  NOV 2019
  • Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Brown, Peter; Tan, Aik-Choon; El-Esawi, Mohamed A.; Liehr, Thomas; Blanck, Oliver; et al.
    Database-the Journal Of Biological Databases And Curation DOI: 10.1093/database/baz085 OCT 2019
Julia Vorholt

Prof. Dr. Julia Vorholt
ETH Zurich
Institute of Microbiology
8093 Zurich

Tel: +41 (0)44 632 55 24

Research topics

  • Metaproteome/-genome analysis of microbial communities
  • Synthetic bacterial communities
  • Plant probiotics
  • Identification of traits important for phyllosphere colonization
  • General stress response in Alphaproteobacteria
  • One carbon metabolism



  • Microbial community analyses
  • Proteomics
  • Metabolomics
  • Microscopy (FISH)
  • Single cell manipulation using FluidFM technology