Focus on the intestinal microbiota

Research topics of the RG Deppenmeier

The research subjects include:

  • Physiology and biochemistry of the most important representatives of the human gut microbiota
  • microbial production of succinate as a platform chemical from sustainable materials
  • microbial production of prebiotics and low-calorie sweeteners
  • mechanisms of energy conservation in methanogenic archaea and the function of the organisms in biogas plants

Physiology and biochemistry of the human gut microbiota

The human gut microbiota is as a crucial environmental factor that plays a major role in host physiology by affecting several processes ranging from maturation of the immune system, regulation of host metabolism and nutritional effects to transformation of bioactive compounds and many more. Increasing evidence indicates the impact of changes in the composition of the human gut bacteria on host metabolism and a variety of diseases. To analyze these effects it is necessary to measure the function and metabolic activity of the intestinal bacteria. It is necessary to combine bioinformatic predictions and biochemical realities, which is the main goal of our approach to characterize the human gut microbiome. Current research projects concern the production of succinate as promising precursor for the production of bio-plastics and the analysis of the gut microbiota with respect to the formation of dangerous chemical substances (e.g. nitrosamines and modified xenobiotics). Also the whole range of molecular biological techniques is involved to give us a comprehensive understanding of how these organisms thrive.

Darmmikrobiota EN
© Natalie Hager
Eine Wissenschaftlerin und ein Wissenschaftler arbeiten hinter einer Glasfassade und mischen Chemikalien mit Großgeräten.
© Volker Lannert

Production of prebiotics and low-calorie sweeteners

It is known that excessive consumption of sugar can lead to food-associated diseases in humans. The introduction of low calorie- sugar derivatives is therefore of great public interest.  Furthermore, there is a need for enzymatic synthesis of dietary fibers, which have prebiotic effects. These non-digestible fibers can also be used to increase viscosity of food, to improve organoleptic properties, and could also function as fat substitutes. Our research group collaborates with the RTWH Aachen, the FZ Jülich, and the Pfeifer & Langen GmbH and Co. KG to establish biotechnological production routines for prebiotic and/or low- calorie, sweet-tasting carbohydrates. The collaboration is focused on the synthesis and validation of levan- and inulin-based di-, oligo- and polysaccharides, promising functional compounds with application in food, medical and agricultural sectors. The microbial and enzymatic processes are based on sustainable and renewable raw materials such as sucrose and starch to support a future-oriented economy. Our research includes the search for promising biocatalysts, the application of molecular cloning techniques, enzyme characterization as well as the optimization of microbial production platforms and cultivation strategies.

Biotransformation by acetic acid bacteria

Gluconobacter oxydans is a Gram-negative acetic acid bacterium with significant biotechnological potential. Acetic acid bacteria, in general, can efficiently convert various carbohydrates and alcohols into valuable compounds, including l-ascorbic acid (vitamin C), miglitol, dihydroxyacetone, and gluconic acids, which have applications in the food, pharmaceutical, and chemical industries. In our group, efficient molecular tools were developed for the genetic modification and optimization of Gluconobacter sp. (e.g., plasmid-mediated gene expression, markerless gene deletion, genome engineering). These tools are exploited in our lab to create a variety of tailor-made Gluconobacter strains capable of synthesizing value-added compounds from renewable and sustainable resources. Numerous sugar-modifying enzymes have already been identified and applied for the synthesis of levan, levan-based fructooligosaccharides, xylan-based fructooligosaccharides, and 5-keto-d-fructose after homologous or heterologous production in G. oxydans or closely related acetic acid bacteria. Product concentrations and space-time yields are further maximized by optimizing production strains, fermentation conditions, and overall process management. Products of Gluconobacter-mediated biotransformation are purified by appropriate methods and characterized with respect to potential applications.

Gluconobacter oxydans
© Prof. Dr. Uwe Deppenmeier
© Bioreact GmbH (Troisdorf)

Mechanisms of energy conservation in methanogenic archaea

The process of methanogenesis is important for the global carbon cycle because it represents the terminal step in the anaerobic breakdown of organic matter. Large amounts of methane escape into the atmosphere and act as greenhouse gas but are also used as renewable energy source in biogas facilities. We focus on methanogenic archaea that are associated with the human microbiota. A representative of these human-associated organisms is Methanomassiliicoccus luminyensis, which uses methylamines as substrates with H2 serving as reductant. In this way the organism reduces the concentration of trimethylamine and its follow-up products. This process leads to a reduction of trimethylamineoxide formation and prevents the deleopment of atherosclerosis. We mainly focus on enzymes and enzyme complexes that are involved in the energy metabolism in M. luminyensis. Additionally, the growth behavior of the organism is part of our research interests to gain insights of how the organism persists and grows in the human intestines. Many techniques are involved in this research, ranging from proton translocation measurements to anaerobic protein purification.


 Here you can find a list of our previously published papers.


Here you can find a list of the current members of the research group.

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