Experimental Biogas Research
We run lab-scale biogas reactors to study selected aspects of biogas production. Besides standard process analytics, we assess microbial community dynamics via metagenomics, metatrancriptomics, metaproteomics, flowcytometry, and microcalorimetry.
Contact:Fabian Bonk, Daniela Taraba, Denny Popp, Florian Centler
Partner:Sabine Kleinsteuber, Heike Sträuber, Thomas Maskow, Martin von Bergen, Nico Jehmlich, Susann Müller
Modeling Microbial CommunitiesWe develop mathematical models describing the dynamics of microbial communities, focussing on metabolic transformation processes. Both ordinary-differentail-equation-based and Flux-Balance-Analysis approaches, and combinations of both, are used.
Contact:Florian Centler, Denny Popp, Fabian Bonk
Partner:Steffen Klamt (MPI Magdeburg), Sabine Koch (MPI Magdeburg), Dirk Benndorf (Uni Magdeburg), Sören Weinrich (DBFZ)
Spatio-temporal ModelingSpace plays an essential role for natural microbial systems. Within the TWIN-Project, we develop experimental systems and spatio-temporal models for studying functional stability and resilience. Individual-based modeling approaches are used for analyzing bacteria-bacteria and bacteria-fungi interactions.
Kooperationspartner:Lukas Wick, Martin Thullner, Karin Frank, Thomas Banitz, Sara König, Tom Berthold, Matthias Kästner, Anja Miltner, Anja Worrich
Network analysis of microbial communitiesSpatial and temporal data on microbial community composition can provide evidence for principles of the organization of microbial life. The complex interplay at work can be visualized by co-occurrence analysis-derived networks, which can be explored by methods from network analysis and data-mining.
Kooperationspartner:Annelie Wendeberg, Annelie Steinbach, Torsten Jeske, Lukas Wick, Michael Schloter (Helmholtz-Zentrum München)
In Silico Metabolic EngineeringDetails under "M.Sc. topics" below.
Within the HIGRADE PhD program, we offer a one-day introductory Systems Biology course in cooperation with the Department Molecular Systems Biology: Introduction to Systems Biology: From OMICS data analysis to metabolic network modeling. Details available at the HIGRADE website.
The next course is in September 2018.
Further contributions to teaching activities:
HIGRADE course Fluxomics - Quantifying the Metabolic Phenotype (23rd/24th of May 2018 - Florian Centler)
TU Dresden Continuous Bioprocesses: Anaerobic Digestion - Lecture and exercise (WS 2017/2018 - Denny Popp)
University Leipzig Quantitative Biology for a sustainable enrivonmental and industrial biotechnology - Several lectures and exercise (SS2018 - Florian Centler, Denny Popp)
Master students: Sophia Klink, Tatjana Malycheva, Stefan Bauer, Paul Jähne, Lukas Hirsch
Bachelor students: Robin Goldmann, Eric Witt
Interns: Piotr Jachimowicz, Amit Nain, Ahmad Zino
- Outstanding Poster Award - 15th IWA World Conference on Anaerobic Digestion (AD15-2017), October 2017, Beijing, China
- Young Investigator Group Award - e:Bio Status Seminar 2017 BMBF, September 2017, Dresden, Germany
- Best Poster Pitch - HIGRADE Conference 2017, May 2017, Leipzig, Germany
- Best Poster Prize - 3rd International Conference on Biogas Microbiology (ICBM3), May 2017, Wageningen, The Netherlands
- Best Poster Slam - 3rd International Conference on Monitoring and Process Control of Anaerobic Digestion Plants, March 2017, Leipzig, Germany
We are offering research topics in the area of mathematical modeling, analysis of microbial communities and biogas reactor experiments. Please contact us if you are interested in the simulation of metabolic networks, network analysis, indiviudal-based modeling, or the development of bioinformatic tools. Besides theoretical topics, wet lab related topics are also available, find more details here.
Master thesis: "Construction of metabolic network models from genome data" Eric Witt, University Leipzig
Annotated genomes retrieved from metagenomes will used to reconstruct metabolic networks. The generated networks will be simulated by flux balance analysis and results compared with literature knowledge.
Master thesis: "Bioinformatic analysis of flow cytometry data on biogas processes" Sebastian Luhnburg, University Leipzig
Data from biogas processes analyzed with flow cytometry will be evaluated and compared with the results from molecular biological approaches.
Master thesis: "Phages in anaerobic digestion" Hamna Saleem, University Jena
Phages and their impact on the microbial communities in anaerobic digesters are rarely studied. Metagenomic sequencing will be used to characterize phages in biogas reactors. (in cooperation with the group Microbial Systems Ecology)
Master thesis: "Biogas production at very low hydraulic retention times" Stephanie Otto, Hochschule für angewandte Wissenschaft und Kunst Hildesheim/Holzminden/Göttingen University of Applied Sciences and Arts
The hydraulic retention time of anaerobic digesters producing biogas from short-chain fatty acids will be decreased until process failure. The process parameteres and the microbial communities will be monitored.
Tatajana Malycheva: "Anaaerobic digestion of propionic acid: Dynamics of microbial communities and kinetics of propionic acid oxidation", master thesis, Saarland University
Sophia Klink: "Molecular Biological Analysis of Biogas Reactors under Ammonia Inhibition", master thesis, Ludwig Maximilian University of Munich
Stefan Bauer: "Comparison of methods for quantification of biomass from a biogas reactor", master thesis, University of Kassel
Robin Goldmann: "Molecular biological analysis of microbial communities in biogas reactors", bachelor thesis, Leipzig University
Paul Jähne: "Optimization of in silico metabolic engineering strategies with evolutionary algorithm using CUDA", master thesis, Leipzig University of Applied Sciences
Lukas Hirsch: "Using dynamic modeling to infer microbial interaction networks from flow cytometry data", master thesis, Leipzig University
Eric Witt: "Molecularbiological characterization of microbial communities in biogas reactors", bachelor thesis (in cooperation with the group Microbiology of Anaerobic Systems), Leipzig University