Systems Biology of Microbial Communities

Metabolism-centered Predictive Modeling of Anaerobic Digestion for Biogas Production (McBiogas)

McBiogas Logo
Photo: Sebastian Wiedling

Research Topic

Microorganisms typically occur as highly divers communities in nature. This allows for a multiude of interactions to occur between members of the community and makes complex transformation processes possible. Anaerobic digestion is a typically example for such a community-driven process in which organic material is transformed to methane. To optimally control this process in biogas plants, mathematical models have been developed. These models, however, typically only consider major process steps und do not directly consider the high phenotypic diversity of involved communities. Both their composition and activity can today be assessed with high accuracy by culture-independent methods including metagenomics, metatranscriptomics, and metaproteomics. Our aim is to use such data to create mathematical models detailing the metabolic transformation network within microbial communities. Towards this end, species-specific metabolic network models are inferred and coupled to a dynamic community model following the dynamic Flux-Balance-Analysis approach. Due to their predictive power, such models will be used to early detect looming process breakdowns and to initiate proper counter measures, as well as to explore the potential for flexibel on-demand biogas production.

Following a Systems Biology approach, the McBiogas project requires the close interdisciplinary cooperation between experimental and theoretical work. We use lab-scale biogas reactors as our experimental system, develop bioinformatic methods for the inference of metabolic network models, and design and implement modeling software for the simulation of microbial communities.


Eric Witt

Sebastian Luhnburg

Hamna Saleem

Stephanie Otto


Emine Ceren Özveri

Salomé Herbin


Student assistants

Tatjana Malycheva

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.

Fabian Bonk, Daniela Taraba, Denny Popp, Florian Centler
Sabine Kleinsteuber, Heike Sträuber, Thomas Maskow, Martin von Bergen, Nico Jehmlich, Susann Müller

Modeling Microbial Communities

We 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.
Florian Centler, Denny Popp, Fabian Bonk
Steffen Klamt (MPI Magdeburg), Sabine Koch (MPI Magdeburg), Dirk Benndorf (Uni Magdeburg), Sören Weinrich (DBFZ)

Spatio-temporal Modeling

Space 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.
Florian Centler
Lukas Wick, Martin Thullner, Karin Frank, Thomas Banitz, Sara König, Tom Berthold, Matthias Kästner, Anja Miltner, Anja Worrich

Network analysis of microbial communities

Spatial 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.
Florian Centler
Annelie Wendeberg, Annelie Steinbach, Torsten Jeske, Lukas Wick, Michael Schloter (Helmholtz-Zentrum München)

In Silico Metabolic Engineering

Details 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

Student assistants: Tarek M.M. Hamed Elzamel, Vivien Wieczorek, Athaydes Francisco Leite, Daniela Pietzsch, Malte Stadtmann, Josephine Hörner, Nicole Thiemich

Mcbiogas for the win
McBiogas and his team won the poster slam at the 3rd International Conference on Monitoring and Process Control of Anaerobic Digestion Plants! (c) DBFZ

  • 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

Open topics

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.


Current topics

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.

Completed topics


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


This group is funded by the BMBF.