James Marsh

Microbiome engineering

Max Planck Institute for Biology
Adjunct faculty in: IMPRS


  • PhD, Institute for Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia, 2011-2015
  • Postdoc, the i3 institute, University of Technology Sydney, NSW, Australia, 2015-2018
  • Postdoc, Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany, 2018-2021
  • Project Leader at the MPI for Biology in the Department of Microbiome Science since 2021

Research Interest
The community of microorganisms within the human gastrointestinal tract is one of the most diverse ecosystems known, yet we currently have limited tools to unravel its intrinsic complexity. Next-generation sequencing approaches have been invaluable for the characterization of gut microbial distribution, abundance, and evolution, but elucidating the mechanistic basis for these dynamics requires an ability to perturb the system through manipulation and testing. By developing novel microbiome engineering techniques, we are genetically reprogramming diverse, non-model organisms associated with the human gut to understand both their ecological niche and the interactions that drive emergent properties of the community. Our key research goals include:

  • The development of microbiome-specific tools for the precise, tunable manipulation of taxonomically diverse, non-model organisms, both in single organism and community contexts.
  • The genetic manipulation of keystone species associated with the human gut microbiome to identify genetic determinants for colonization, metabolism, and community interactions.
  • Microbiome engineering of complex communities for functionally characterizing the community-level consequences of single gene perturbations.

These research priorities are driven by a combination of bioinformatic and wet-laboratory efforts. We rely heavily on the isolation and cultivation of aerobic and anaerobic organisms, advanced molecular microbiology and engineering techniques to develop genetic tools, and short- and long-read sequencing to generate large genomic and metagenomic datasets. These data are analyzed using existing bioinformatic approaches that have been developed in the laboratory, and we are applying emerging machine-learning-based applications to develop novel pipelines to support these goals.

Available PhD Projects 

  • Currently not recruiting PhD students

Selected Reading

  • Marsh, J.W., Kirk, C., and Ley, R.E. (2023). Toward microbiome engineering: Expanding the repertoire of genetically tractable microbes of the human gut microbiome. Annual Review of Microbiology (accepted).
  • Marsh, J.W. and Ley, R.E. (2022). Microbiome engineering: Taming the untractable. Cell 185:3.
  • Hayward, R.J., Marsh, J.W., Humphrys, M.S., Huston, W.M., Myers, G.S.A. (2020). Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. Epigenetics & Chromatin 13:45.
  • Hayward, R.J., Marsh, J.W., Humphrys, M.S., Huston, W.M., Myers, G.S.A. (2019). Early transcriptional landscapes of Chlamydia trachomatis-infected epithelial cells at single cell resolution. Frontiers in Cellular and Infection Microbiology 9:392
  • Marsh, J.W., Hayward, R., Shetty, A., Mahurkar, A., Humphrys, M.S., and Myers, G.S.A. (2017). Bioinformatic analysis of bacteria and host cell dual RNA-Sequencing (dRNA-Seq) experiments. Briefings in Bioinformatics bbx043.
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