Phd-position

The Max Planck Society is one of Europe's leading research organizations and conducts basic research in the natural sciences, life sciences, and humanities. The Max Planck Institute for Chemical Ecology in Jena carries out fundamental research on how organisms communicate with each other via chemical signals. We analyze ecological interactions with molecular, chemical and neurobiological techniques. In the Institute, organic chemists, biochemists, ecologists, entomologists, behavioral scientists, insect geneticists and physiologists work in collaboration to unravel the complexity of chemical communication that occurs in nature.
Applications are invited for a
**PhD Project**:
Decoding Symbiont Establishment through Systems Modeling and Multi-Omics Integration
**Supervisors**:
Dr. Mariana Galvão Ferrarini, Prof. Dr. Martin Kaltenpoth, and Dr. Tobias Engl Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena
Background
The establishment of stable symbiotic relationships between insects and bacteria involves complex exchanges of metabolites, regulatory signals, and evolutionary adaptations. Understanding these processes requires integrating diverse layers of biological information - from genomes and transcriptomes to metabolomes - into coherent systems-level models. The long-term association between the grain beetle Oryzaephilus surinamensis and its bacterial endosymbiont Shikimatogenerans silvanidophilus represents a model for nutritional symbiosis, where the bacterium supplies compounds essential for the host’s fitness. In nutrient-limited environments such as stored grains, these metabolic contributions become critical. Our group has recently shown that a free-living bacterium Sodalis praecaptivus can replace the resident endosymbiont, offering an experimentally tractable system to investigate how novel partnerships are established and maintained. Building on these findings, this project adopts a systems biology perspective, integrating metabolic and regulatory network modeling with multi-omics data to uncover the principles governing host-symbiont equilibrium and the emergence of new symbiotic associations.
Project Description and Research questions
Through computational modeling and data integration, this project aims to explore the molecular basis of metabolic exchanges and regulatory interactions between the host and its bacterial partners. A particular focus lies on how these interactions evolve and stabilize during symbiont establishment. Model-based predictions will be further refined and experimentally tested, ensuring an iterative exchange between in silico and in vivo approaches. Key research questions include:
1. How does metabolic complementarity change during symbiont establishment?
2. Which metabolic reactions are indispensable for maintaining host-symbiont equilibrium?
3. Can we predict ways to make Sodalis praecaptivus less virulent?
4. How do regulatory layers modulate metabolic fluxes under symbiotic versus free-living conditions?
Objectives and Methodology
- Genome-scale metabolic network reconstruction of the partners and model refinement;
- Assignment of potential functions to hypothetical proteins with the use of AI-based structure prediction tools;
- Host-symbiont metabolic integration and simulation of exchange fluxes;
- Topology and constraint-based modeling including prediction of essential genes with in silico knockouts;
- Interventions and detection of vulnerabilities with the enumeration methods;
- Genome-wide regulatory network reconstruction and metabolic integration;
- Integration of diverse omics data (available and to be acquired);
- Comparative genomics across diverse insect symbioses.
- critical scientific thinking skills
- a deep interest in the evolutionary and molecular biology of insect-microbe interactions
- a strong background in computational biology and/or coding ability
- attention to detail to handle command line tools and programming scripts
- collaborative spirit, curiosity, and creativity
- time management and organizational skills
- proficiency in written and spoken English as well as good communication skills

Further reading
Nielsen J. Systems Biology of Metabolism. Annu Rev Biochem., 20, 245-275 (2017).
Ankrah N. et al. Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling. J Bacteriol, 199:10.1128/jb.00872-16 (2017).
Engl, T. et al. Ancient symbiosis confers desiccation resistance to stored grain pest beetles. Mol. Ecol. 27, 2095-2108 (2018).
Kiefer J. et al. Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis. Commun Biol., 11; 4(1): 554 (2021).
Wodak et al. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annual Reviews, Vol 52:183-206. (2023).
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