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Laboratory of Microbial Processes


The main topics:

  • Aerobic and anaerobic cultivation of bacteria, yeasts, and filamentous fungi
  • Production of primary and secondary metabolites
  • Characterization of microbial populations by use of fluorescent techniques
  • Molecular biology of solventogenic clostridia
  • Production of secondary metabolites by the fungus Monascus



Main research topics

Production of biofuels and bioplastics

Biotechnological production of biofuels (ethanol and butanol) and bioplastics precursors (succinic acid, lactic acid) by using first and second generation feedstocks. Design of fermentation process, selection of suitable feedstock, cultivation conditions and process arrangements (batch, fed-batch, continuous) for maximum yield and process productivity.  

Molecular biology of solventogenic clostridia

Analysis of gene function and comparative genome studies focused on the basic research of the organic solvents biosynthesis during acetone–butanol–ethanol (ABE) fermentation. Methods for genetic manipulation of solventogenic clostridia development, qPCR based gene expression monitoring and description of the biobutanol biosynthesis on the molecular level. Endospore formation research of Clostridium bacteria.

Analysis of microbial populations on the single cell level

Detailed analysis of microbial populations using fluorescent microscopy, flow cytometry, and fluorimetry. Analysis of cell viability, growth rate, enzyme activities, concentration of intracellular compounds (DNA, NA, proteins, PHA, GFP, …) and other cell functions using selective staining with fluorescent probes. Measurement of these parameters for bacterial and yeast populations within the cultivation process under the influence of stress factors and antimicrobial agents.

Production of recombinant proteins by microbial host strains

Use of continuous processed data for the design of fed-batch processes for high cell density cultivation for production of recombinant proteins. Analysis of online and offline variables, design of suitable process arrangement.

Processing of waste materials from agriculture and industry into value-added products

Physico-chemical and/or enzymatic processing of lignocellulosic materials (wheat, wood, etc.) and keratin rich material (e.g. chicken feathers) and use of substrates based on nutrients derived from these feedstocks for biotechnological production of value-added products, e.g. biofuels (bioethanol, biobutanol), precursors of bioplastics (lactic and succinic acids), and others.

Production of secondary metabolites

Production of oligoketide pigments by Monascus purpureus by solid state or submersed cultivation. Optimization of cultivation conditions for preferential biosynthesis of yellow pigments (monascin and ankaflavin). Isolation and determination of pigments, citrinin, and monacolin K. Testing the effects of yellow pigments on the rat metabolic syndrome (in cooperation with ICEM).  


Updated: 27.6.2019 14:02, Author: Martin Halecký

Selected Results

Patáková P. et al., Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level, Scientific Reports 9, 1371, 2019 (on-line)

Sedlar K. et al., Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq. BMC Genomics 19 (1), 415, 2018 (online)

Branska B. et al., Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions. Biotechnology for Biofuels 11:99, 2018 (online)

Patakova P., Kolek J., Sedlář K., Koscova P., Branska B., Kupkova K., Paulova P., Provazník I.: Comparative analysis of high butanol tolerance and production in clostridia, Biotechnology Advances 36(3),721-738, 2018 (online)

Sedlar K., Kolek J., Provaznik I., Patakova P.: Reclassification of non-type strain Clostridium pasteurianum NRRL B-598 as Clostridium beijerinckii NRRL B-598. Journal of Biotechnology 244(20), 1-3 (2017) (online)

Kolek J., Sedlar K., Provaznik I., Patakova P. Dam and Dcm methylations prevent gene transfer into Clostridium pasteurianum NRRL B-598: development of methods for electrotransformation, conjugation and sonoporation. Biotechnology for Biofuels (2016) 9:14.DOI 10.1186/s13068-016-0436-y, (open access)

Paulová L., Patáková P., Branská B., Rychtera M., Melzoch K.: Lignocellulosic ethanol: Technology design and its impact on process efficiency. Biotechnology Advances. doi:10.1016/j.biotechadv.2014.12.002 (online)

Kolek J., Patakova P., Melzoch K., Sigler K., Řezanka T. Changes in membrane plasmalogens of Clostridium pasteurianum during butanol fermentation as determined by lipidomic analysis. PLOS ONE 10.1371/journal.pone.0122058 (2015)

Patáková P., Linhová M., Vykydalová P., Branská B., Rychtera M., Melzoch K.: Use of fluorescent staining and flow cytometry for monitoring physiological changes in solventogenic clostridia. Anaerobe 29: 113-117 (2014), ISSN 1075-9964, IF 2,022 (online)

Paulova L., Hyka P., Branska B., Melzoch K., Kovar K.: Use of a mixture of glucose and methanol as substrates for the production of recombinant trypsinogen in continuous cultures with Pichia pastoris Mut(+). Journal of Biotechnology 157 (1): 180-188 (2012). (online)

Patáková P.: Monascus secondary metabolites: production and biological activity. Journal of Industrial Microbiology and Biotechnology 40(2): 169-181. (2013) (online)

Paulová L., Patáková P., Rychtera M., Melzoch K.: High solid fed-batch SSF with delayed inoculation for improved production of bioethanol from wheat straw. Fuel 122: 294-300. (2014) IF 3,406 (online)


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