PhD Position (m/f/d) | Decoding symbiont establishment through systems modeling and multi-omics[...]

Stellenbeschreibung:

PhD Position (m/f/d) | Decoding symbiont establishment through systems modeling and multi-omics integration

Join the Max Planck Institute for Chemical Ecology in Jena to decode the establishment of stable symbiotic relationships between insects and bacteria. The PhD project will integrate genome, transcriptome, metabolome, and regulatory network data into systems-level models to uncover the principles governing host‑symbiont equilibrium.

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 grain beetle Oryzaephilus surinamensis and its bacterial endosymbiont Shikimatogenerans silvanidophilus serve as a model for nutritional symbiosis. Recent work demonstrated that the free‑living bacterium Sodalis praecaptivus can replace the resident endosymbiont, providing an experimentally tractable system to study how novel partnerships are established and maintained. The PhD project builds on these findings by integrating metabolic and regulatory network modeling with multi‑omics data.

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 refined and experimentally tested, ensuring an iterative exchange between in silico and in vivo approaches.

How does metabolic complementarity change during symbiont establishment?
Which metabolic reactions are indispensable for maintaining host‑symbiont equilibrium?
Can we predict ways to reduce the virulence of Sodalis praecaptivus ?
How do regulatory layers modulate metabolic fluxes under symbiotic versus free‑living conditions?

Objectives and methodology

The specific objectives will be defined jointly with the candidate, based on their interests and background.

Genome‑scale metabolic network reconstruction of partners and model refinement;
Assignment of potential functions to hypothetical proteins using 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;
Identification of vulnerabilities with 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.

Candidate profile

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 in handling command line tools and programming scripts;
Collaborative spirit, curiosity, and creativity;
Time management and organizational skills;
Proficiency in written and spoken English and good communication skills.

Your application

Deadline for Application: Dec 15th 2025. The Max Planck Society is committed to gender equality and diversity, actively supports work‑family balance, and encourages applicants with severe disabilities. We welcome applications from all backgrounds. Please apply via our application portal and submit your complete application documents.