The Zeller Lab

Microbiome Systems Biology

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 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.

Recent Papers
ATF6 activation alters colonic lipid metabolism causing tumour-associated microbial adaptation
Coleman OI, Sorbie A, Riva A, von Stern M, Kuhls S, Selegato DM, Siegert L, Keidel I, Kohler N, Wirbel J, Kacprowski T, Dunkel A, Pauling JK, Plagge J, Mediel-Cuadra D, Wagner SJ, Chadly I, Bierwith S, Peng T, Metzler T, Li X, Heikenwalder M, Schafmayer C, Hinz S, Roder C, Rocken C, Zimmermann M, Rosenstiel P, Steiger K, Jesinghaus M, Liebisch G, Ecker J, Schmidt C, Zeller G, Janssen KP, Haller D, Nat Metab (2025).
Published 01 Sep 2025
PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity
Larralde M, Zeller G, Carroll LM, NAR Genomics and Bioinformatics 7 (3) (2025).
Published 11 Jul 2025
[PREPRINT] Fast, flexible gene cluster family delineation with IGUA
Larralde M, Blom J, Gourle H, Carroll LM, Zeller G, biorxiv (2025).
Published 19 May 2025
Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease
Romano S, Wirbel J, Ansorge R, Schudoma C, Ducarmon QR, Narbad A, Zeller G, Nat Commun 16 (1) :4227 (2025).
Published 07 May 2025
[PREPRINT] Machine learning inference of natural product chemistry across biosynthetic gene cluster types
Larralde M, Zeller G, biorxiv (2025).
Published 15 Mar 2025
Projects
Inferring gene functions (using AI)
Can we predict the function of microbial genes – even if we know little about the organisms themselves?
Statistical modelling and meta-analyses
How to effectively utilise statistical modelling and machine learning to delineate microbiome-disease signatures and identify robust biomarkers for disease diagnosis and prognosis?
Spatial community analysis
How to image diverse microbial communities in their natural environment to reveal spatial community architectures?
Gut microbial secondary metabolism
How does gut microbial secondary metabolism impact human diseases and drug treatments?
Microbiome profiling
How can we accurately identify and quantify microbes and their gene functions from various sequencing readouts including ones generated from low-biomass samples?
Intratumoral microbiome
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?
Gut dysbiosis / disease associations
Can we obtain a quantitative understanding of gut dysbiosis to rationalise microbiome modulation?
Dietary interventions and microbiome modulation
How can the microbiome be modulated to improve human health?
News