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:Denny Popp, Daniela Taraba, 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
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.
Ecological Stability Properties
In colaboration with our flow cytometry experts, we developed an R-script that assesses a microbial community's response to a disturbance over time, computing numerical values for resistance and resilience, among other stability properties. Developed with flow cytometric data in mind, it is equally applicable to any OMICS data which provides relative abundance time series data. Read more in our open access publication. Get the script at GitHub.
Infering Interaction Networks
Data on microbial community structure and its evolution over time are routinely recorded today. Can such data be used to infer microbial interactions? We developed an R package that takes such data and fits interaction matrices of generalized Lotka-Volterra models. Additionally, the package allows for the generation of in silico data with known interactions to assess the correctness of inferred interaction networks.
Get the R package at GitHub.
Reactive Flow and Transport Simulator
Details can be found here.
Denny Popp, Florian Centler. µbialSim: constraint-based dynamic simulation of complex microbiomes. bioRxiv doi: 10.1101/716126
Sören Weinrich, Sabine Koch, Fabian Bonk, Denny Popp, Dirk Benndorf, Steffen Klamt, Florian Centler. Augmenting biogas process modeling by resolving intracellular metabolic activity. Frontiers in Microbiology 2019 10:1095 doi: 10.3389/fmicb.2019.01095
Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Daniela Becker, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques. Frontiers in Microbiology. 2019 10:166 doi: 10.3389/fmicb.2019.00166
Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Ammonia inhibition of anaerobic volatile fatty acid degrading microbial communities. Frontiers in Microbiology. 2018 9:2921 doi: 10.3389/fmicb.2018.02921
Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler. Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion. Biotechnology for Biofuels 2018 11:274 doi: 10.1186/s13068-018-1279-5Fabian Bonk*, Denny Popp*, Hauke Harms, Florian Centler. PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. Journal of Microbiological Methods. 2018 153:139-147 doi: 10.1016/j.mimet.2018.09.015 (*contributed equally)
Courses offered by our group:
HIGRADE course Introduction to Systems Biology: From OMICS data analysis to metabolic network modeling.
The next course will be in autumn 2019.
Develop course Introduction to long read sequencing for (meta)genomics.
The next course will be on 16th of January 2020.
Details available at the HIGRADE website.
Further contributions to teaching activities:
HIGRADE course Fluxomics - Quantifying the Metabolic Phenotype (Florian Centler)
TU Dresden Continuous Bioprocesses: Anaerobic Digestion - Lecture and exercise (winter semester - Denny Popp)
University Leipzig Quantitative Biology for a sustainable enrivonmental and industrial biotechnology - Several lectures and exercise (sommer semester - Florian Centler, Denny Popp)
PhD students: Fabian Bonk
Master students: Florian Schmidt, Anna Weimer, Marting Graf, Sebastian Luhnburg, Eric Witt, Stephanie Otto, Sophia Klink, Tatjana Malycheva, Stefan Bauer, Paul Jähne, Lukas Hirsch
Bachelor students: Robin Goldmann, Eric Witt
Interns: James Shields, Salomé Herbin, Emine Ceren Özveri, Hamna Saleem, 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: "Metabolic network reconstruction of microorganisms found in biogas reactors and community-wide flux balance analysis" Jia Fu, Leipzig University
Metabolic network will be reconstructed from metagenome assembled genomes (MAGs) from biogas reactors. Flux balance analysis will be performed of the inidividual as well as community-wide metabolic networks.
Master thesis: "Visualization and interpretation of cross-feeding networks of microbial communities" Jens-Tilman Rau, Leipzig University
Florian Schmidt: "Meta analysis of bacterial communities in biogas reactors", master thesis, Leipzig University
James Shields: "Genome Scale Metabolic Modelling of a Methanogenic Archaeon using a Genome Recovered from a Biogas Reactor", research placement report, University of Glasgow, Scotland
Anna Weimer: "Anaerobic degradation of volatile fatty acids in continuous biogas reactors at very short hydraulic retention times", master thesis, University of Lund, Sweden
Martin Graf: "Integrated analysis of compositional multiomics time series data for the discovery of microbial interactions and metabolic networks", master thesis, Osnabrück University
Sebastian Luhnburg: "Characterization of microbical communities by combined analysis of flow cytometry and amplicon sequencing data", master thesis, Leipzig University
Eric Witt: "Creation of metabolic network models from genome data", master thesis, Leipzig University
Stephanie Otto: "Anaerobic degradation of volatile fatty acids in biogas reactors at very short hydraulic retention times", master thesis, Hochschule für angewandte Wissenschaft und Kunst Hildesheim/Holzminden/Göttingen University of Applied Sciences and Arts
Tatjana 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