The Zeller Lab is a human microbiome research group aimed at gaining a better fundamental understanding of the human microbiome and exploring the clinical relevance of its complex interactions with the host using various systems biology approaches. The group, led by Georg Zeller, is based at the Leiden University Medical Center in Leiden, Netherlands, and belongs to the Microbiome & Health Cluster of the Leiden University Center for Infectious Diseases (LUCID).

The Zeller Lab combines sequencing and imaging approaches with computational and statistical analysis techniques to study the composition, function and spatial organisation of the human microbiome. Our work aims to elucidate how the human microbiome impacts human health and disease. We strive for a more quantitative understanding of how host factors shape the microbiome (e.g. diet or medication), how microbes contribute to disease processes (e.g. cancer formation) and how we can harness microbiome modulation to restore human health or improve medical treatments.

To achieve these goals, we collaborate across disciplines with microbiologists, data scientists and clinicians. We embrace open science principles to promote reproducible (computational) research. We value diversity and inclusivity in an international team of researchers with diverse educational and cultural backgrounds. If you would like to learn more or are interested in working with us, please contact us.

Leiden is a vibrant, multicultural city with the Leiden Bio Science Park being one of Europe’s largest and most dynamic research environments hosting both excellent academic institutes and biomedical companies. Other cultural and scientific hubs, such as Den Haag, Amsterdam, Delft, Rotterdam and Utrecht are very close by, making Leiden an ideal place for working and living.

Health benefits of a five-day at-home modified fasting program: a randomised controlled trial
Grundler F, Ducarmon QR, Holley A, Knufinke M, Strathmeyer S, Heelemann S, Geyer R, Martinez-Tellez B, MacArthur MR, Zeller G, Wilhelmi de Toledo F, Mesnage R, Genome Med 18 (1) (2026).
Published 01 Jun 2026
[PREPRINT] Decoding the diet–gut–liver axis: links between dietary pattern adherence, gut microbiome, and hepatic health
Deng K, Ducarmon QR, Godneva A, Zhang Z, van Hylckama Vlieg A, Rosendaal FR, Zeller G, Segal E, Li-Gao R, DIYUFOOD consortium, medRxiv (2026).
Published 10 May 2026
Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires
Ducarmon QR, Karcher N, Giri S, Tytgat HLP, Delannoy-Bruno O, Pekel S, Springer F, Worz P, Schudoma C, Typas A, Zeller G, Nat Microbiol (2026).
Published 24 Apr 2026
[PREPRINT] Machine Learning Identifies Microbiome and Clinical Predictors of Sustained Weight Loss Following Prolonged Fasting
Kaufhold GN, Bartolomaeus TUP, Kraeker K, Schuette T, Kamboj S, Loeber U, Rahn G, McParland V, Braun L, Marko L, Mammadli M, Krannich A, Bahr LS, Gutmann F, Paul F, Ducarmon QR, Zeller G, Mesnage R, Wilck N, Zernecke A, Oefner PJ, Gronwald W, Mueller DN, Forslund SK, Baehring S, Bartolomaeus H, Siebert N, medrxiv (2026).
Published 30 Mar 2026
How to set up and manage a microbiome research facility
Henderickx JGE, Smits WK, Zeller GF, Kuijper EJ, Clin Microbiol Infect (2026).
Published 14 Feb 2026
Can we predict the function of microbial genes – even if we know little about the organisms themselves?
How to effectively utilise statistical modelling and machine learning to delineate microbiome-disease signatures and identify robust biomarkers for disease diagnosis and prognosis?
How to image diverse microbial communities in their natural environment to reveal spatial community architectures?
How does gut microbial secondary metabolism impact human diseases and drug treatments?
How can we accurately identify and quantify microbes and their gene functions from various sequencing readouts including ones generated from low-biomass samples?
In which cancers does an intra-tumoral microbiome exist and how does it interact with other cellular and molecular features of the tumour and its microenvironment?
Can we obtain a quantitative understanding of gut dysbiosis to rationalise microbiome modulation?
How can the microbiome be modulated to improve human health?