Marie-Madlen Pust

I am a microbial ecologist by training, Kennedy Trust for Rheumatology Research (KTRR) Principal Investigator at the Kennedy Institute since 2026, and visiting scientist at the Broad Institute.

My group takes an ecological view of the human microbiome, studying (i) how healthy and inflamed host environments, their metabolic resources and stressors, drive bacterial function, (ii) how the functional state is (epi-)genetically encoded, regulated and memorised within microbial communities and (iii) how it feeds back to shape host interactions and the ecosystem. By combining software development and deep graph learning across multi-omics with experimental microbiology, we uncover causal principles of microbiome function and harness them to engineer microbiomes toward target functions.

During my PhD in Burkhard Tümmler’s lab (2018-2022), supported by the German Academic Scholarship Foundation at the Hannover Biomedical Research School, within the DFG Cluster of Excellence RESIST, I studied how the airway microbiome develops and adapts to the host environment in early human life, modelling microbiome stability and its consequences for immune system maturation, while Nanopore RNA sequencing revealed that beyond species and gene repertoires, microbial gene regulation and structural genome variations are key determinants of bacterial function.

From 2022-2026, I joined Ramnik Xavier’s lab at the Broad Institute, where, together with Kenya Honda’s team, we showed that commensal bacterial guilds suppress antibiotic-resistant Klebsiella through nutrient competition. Donor strains with similar gene content differed in their competitive function, motivating my focus on the regulatory mechanisms that translate environmental context into bacterial phenotypes. Supported by a DFG Walter Benjamin Fellowship (2023–2025), I resolved coding and regulatory RNAs from microbial communities, and found the latter disproportionately contributing to dysbiotic microbiome signatures of inflammatory gut diseases, suggesting their utility as new microbiome-based biomarker and therapeutic targets.