Dr. Melanie Schirmer

Emmy Noether Junior Research Group (DFG)

The role of the oral microbiome in the pathogenesis of gastrointestinal diseases

Academic Career and Research Areas

Dr. Schirmer’s research focuses on the human microbiome, which is the large collection of microorganisms that live in and on our body. In many diseases, such as chronic inflammatory bowel diseases and immune diseases, an imbalance of these microbial communities has been observed. The underlying reasons and consequences of this imbalance are largely unknown though. Previous studies have identified changes of the microbiome and disease-associated bacterial species. However, different strains of the same species can substantially differ in their functional capacities. Therefore, it is important to investigate functional and metabolic differences of microbial strains, in order to develop effective therapies and strategies to prevent these diseases. Her group answers these questions with computational analyses of high-dimensional omics data sets in combination with experimental validation of the disease potential of these organisms. This will provide crucial insights into the role of microbial strains in the development and progression of immune and gastrointestinal diseases.

Dr. Melanie Schirmer studied Mathematics at the University of Bonn and the University of Technology Sydney (Australia). She went on to study Bioinformatics and obtained her PhD from the University of Glasgow (Scotland). As a postdoctoral researcher she spent 3 years at the Broad Institute of MIT and Harvard and at the Harvard T.H. Chan School of Public Health working on questions related to the role of the human microbiome in health and disease. After that, she continued to work as a Computational Scientist at the Broad Institute for another 2 years. Since April 2020 she is leading an Emmy Noether research group at the ZIEL Institute for Food & Health.


    • ERC Starting Grant (2022)
    • Emmy Noether Reserach Group, German Research Foundation (2020)
    • Career Development Award of the Crohn's and Colitis Foundation (2018)
    • Certificate of recognition for scientific accomplishment as an early career investigator (The American Gastroenterological Association) (2018, 2017)

    M. Schirmer, L. Denson, H. Vlamakis, E.A. Franzosa, S.M. Thomas, N.M. Gotman, P. Rufo, S.S. Baker, C. Sauer, J. Markowitz, M. Pfefferkorn, M. Oliva-Hemker, J. Rosh, A. Otley, B. Boyle, D. Mack, R. Baldassano, D. Keljo, N. LeLeiko, M. Heyman, A. Griffiths, A. Patel, J. Noe, S. Kugathasan, T. Walters, C. Huttenhower, J. Hyams, R.J. Xavier: „Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course“. Cell Host & Microbe, 2018


    M. Schirmer, E.A. Franzosa, J. Lloyd-Price, L.J. McIver, R. Schwager, T. Poon, A.N. Ananthakrishnan, E. Andrews, G. Barron, K. Lake, M. Prasad, J. Sauk, B. Stevens, R.G. Wilson, J. Braun, L.A. Denson, S. Kugathasan, D.P.B. McGovern, H. Vlamakis, R.J. Xavier, C. Huttenhower: “Dynamics of metatranscription in the inflammatory bowel disease gut microbiome“. Nature Microbiology, 2018


    M. Schirmer, S.P. Smeekens, H. Vlamakis, M. Jaeger, M. Oosting, E.A. Franzosa, R. ter Horst, T. Jansen, L. Jacobs, M.J. Bonder, A. Kurilshikov, J. Fu, L.A.B. Joosten, A. Zhernakova, C. Huttenhower, C. Wijmenga, M.G. Netea and R.J. Xavier: „Linking the human gut microbiome to inflammatory cytokine production capacity“. Cell, 2016


    M. Schirmer, R. D’Amore, U.Z. Ijaz, N. Hall and C. Quince: “Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data“. BMC Bioinformatics, 2016


    M. Schirmer, U. Z. Ijaz, L. D’Amore, N. Hall and C. Quince: „Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform“. Nucleic Acid Research, 2015