Molecular basis and evolutionary dynamics of C. elegans-microbiota interactions

The model nematode Caenorhabditis elegans is associated with a distinct microbial community under natural conditions. Yet, to date, the role of the worm’s microbiota for life history functions and evolutionary fitness is largely unexplored. This collaborative project aims at providing a holistic understanding of C. elegans-microbiota interactions by
(i) dissecting the influence of the microbiota in mediating evolutionary adaptation to environmental stress using experimental evolution;
(ii) analysing the underlying genetics of C. elegans-microbiota interactions through QTL analysis, transcriptomics and functional genetic manipulation;
(iii) assessing the particular role of bioactive peptides and hydrolytic enzymes in shaping the nematode’s microbial associations using genetic and protein-level analyses; and
(iv) characterizing the proteomic basis of the interaction with the help of state-of-the-art proteome analysis techniques.

The proposed work is based on several advantages of the nematode as an experimental system, including the possibility of producing sterile nematodes through routine procedure combined with controlled re-infection experiments. The nematode also allows efficient performance of evolution experiments because of its short generation time and its amenability to cryopreservation for later analyses. Moreover, a versatile toolbox for genetic manipulation and comprehensive genome databases facilitate the cross-level “omics” analysis of C. elegans-microbiota interactions.

Overall, our project is unique in that it uses complementary study approaches and a highly efficient experimental model system to provide a holistic view on host-microbiota interactions that encompasses the involved evolutionary dynamics as well as the underlying processes at genomic, genetic, transcriptomic, proteomic and also biochemical levels. Based on such a cross-disciplinary analysis approach, our results are expected to yield novel insights into how the microbiota affects evolutionary change and how such dynamics are realized at the molecular level.


Julia Johnke

PhD Candidate, Associated Junior Researcher
Kiel University Zoological Institute

Dr. Liam Cassidy

Postdoctoral Researcher
Kiel University Institute for Experimental Medicine

Dr. Carola Petersen

Postdoctoral Researcher, Associated Junior Researcher
Kiel University Zoological Institute



The Natural Biotic Environment of Caenorhabditis elegans.

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Caenorhabditis elegans as a model for microbiome research.

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FeaturedEfficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology.

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Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose.

Treitz C, Enjalbert B, Portais J C, Letisse F, Tholey A (2016); Proteomics., 16(21):2742-2746. doi: 10.1002/pmic.201600303

Antimicrobial effectors in the nematode C. elegans – an outgroup to the Arthropoda.

Dierking K, Yang W, Schulenburg H (2016); Phil Trans R Soc Lond B., 371. doi:

The native microbiome of the nematode Caenorhabditis elegans: Gateway to a new host-microbiome model.

Dirksen P, Marsh SA, Braker I, Heitland N, Wagner S, Nakad R, Mader S, Petersen C, Kowallik V, Rosenstiel P C, Felix M A, Schulenburg H (2016); BMC Biology, 14:38. doi:10.1186/s12915-016-0258-1