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Research Quantitative Microbial Phenotyping

High-Throughput Bioprocess Characterization

Characterization and optimization of microbial bioprocesses at higher throughput becomes an increasingly important part in modern biotechnology. This incorporates fast screening of potential producer strains to derive classical process performance indicators such as product titer, yield and productivity. Moreover, selected candidate strains are further characterized and optimized by testing large parameter spaces with respect to media composition, induction profiles and process control.
We perform high-throughput bioprocess characterization by combining microtiter plate cultivation, lab automation, microbial strain libraries and biological fluorescence markers. The resulting datasets are complementary to cultivation data stemming from classical pilot-scale bioreactor experiments (liter scale) as well novel microfluidic chip experiments (picoliter scale) performed in the Micro Scale Bioengineering Group.
The work is also closely connected to several groups of the Systemic Microbiology providing interesting candidate strains for in-depth quantitative phenotyping.

graphic of topic high-throughput bioprocess characterization

Selected publications

Radek A, Tenhaef N, Müller MF, Brüsseler C, Wiechert W, Marienhagen J, Polen T, Noack S (2017) Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization. Bioresour Technol doi: 10.1016/j.biortech.2017.05.055

Baumgart M, Unthan S, Kloß R, Radek A, Polen T, Tenhaef N, Müller MF, Küberl A, Siebert D, Brühl N, Marin K, Hans S, Krämer R, Bott M, Kalinowski J, Wiechert W, Seibold G, Frunzke J, Rückert C, Wendisch VF, Noack S (2017) Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology. ACS Synth Biol doi: 10.1021/acssynbio.7b00261

Next Generation Omics-Technologies

Quantitative omics-technologies play a key role in driving systems biology to an applied science for metabolic engineering and synthetic biology of microorganisms. Providing quantitative data of the cell’s transcriptome, proteome, metabolome and fluxome opens the opportunity to piecewise unravel the complex regulatory mechanisms underlying all in vivo metabolic processes.
However, for quantitative analyses not only experimental data, but also their measurement errors play a crucial role. The total measurement error of any analytical protocol is the result of an accumulation of single errors introduced by several processing steps.
We focus on the development and optimization of methods for the quantification of intracellular proteins, metabolites and fluxes based on thoroughly analyzing the propagation of all errors during sample processing.
Resulting multi-omics-data are exchanged with the Modeling and Simulation Group to enable their model-based evaluation and meaningful biological interpretation.

Graphic for topic next generation omics-technologies

Selected publications

Kappelmann J, Klein B, Geilenkirchen P, Noack S (2017) Comprehensive and Accurate Tracking of Carbon Origin of LC-Tandem Mass Spectrometry Collisional Fragments for 13C-MFA. Anal Bioanal Chem doi: 10.1007/s00216-016-0174-9

Kappelmann J, Wiechert W, Noack S (2016) Cutting the Gordian knot: Identiability of anaplerotic reactions in Corynebacterium glutamicum by means of 13C-metabolic flux analysis. Biotechnol Bioeng doi: 10.1002/bit.25833

Voges R, Corsten S, Wiechert W, Noack S (2015) Absolute quantification of Corynebacterium glutamicum glycolytic and anaplerotic enzymes by QconCAT. J Proteomics doi: 10.1016/j.jprot.2014.10.008