Interfaculty Institute of Microbiology and Infection Medicine


Dr. Martina Adamek


Martina Adamek studied environmental sciences at Bielefeld University, where she decided to focus on the fields of Microbiology and Biotechnology. She finished her diploma thesis in the Proteome and Metabolome research group at Bielefeld University, where she worked on the biosynthesis of Xanthan gum in Xanthomonas camperstris pv. campestris. For her PhD she moved to the Karlsruhe Institute of Technology (KIT), Institute of Microbiology on Natural and Technical Interfaces (IFG) where she investigated the diversity within the opportunistic pathogenic bacterial species Stenotrophomonas maltophilia and was able to find novel candidate virulence genes of S. maltophilia using comparative genomics. After finishing her PhD she worked as a Postdoc at the University of Heidelberg, Institute of Immunology, developing diverse PCR applications for the use in clinical routine. Her interest in Microbiology brought her to Tuebingen, where her current research is directed at investigating the mechanisms and the evolutionary processes involved in creating the variety of bacterial natural products.


PhD Students

Timo Negri


Timo Negri studied Biosciences at the Heidelberg University and finished his Bachelor thesis in the field of Glycolbiology at the Centre for Organismal Studies Heidelberg. During his Bachelor studies he became interested in the world of microorganisms and therefore decided to conduct his Master studies in Microbiology at the University of Tuebingen. He completed his Master’s degree in the research group of Applied Natural Products Genome Mining, where he investigated different soil types for their microbial natural product biosynthetic potential. Fascinated by the great diversity of natural products, he decided to continue his work as a PhD student. He is interested in investigating and accessing the true microbial biosynthetic capacity of promising soil types. Using culture independent metagenomic approaches he aims at identifying new secondary metabolites with potential therapeutic application from soil metagenomes.


Ahmed Desouky


Ahmed Desouky studied Pharmacy at MUST, Cairo. Obtained a M.Sc. in Microbiology from Friedrich-Schiller University, Jena. He carried out his thesis at Hans-Knoell Institute, Jena, at the group Secondary Metabolism of Predatory Bacteria. His research there was focused on isolation of natural products from the soil bacterium Cupriavidus basilensis, using genome-mining guided approaches, and NMR-spectroscopy. He moved to Tuebingen for his PhD, at the Ziemert group: Applied Natural Products Genome Mining (Institute of Microbiology and Infection Medicine). His interests includes, development of degenerate primers for screening of metagenomes for natural product clusters, and methods for detection and classification of biosynthetic gene clusters.


Mehmet Direnç Mungan


Mehmet Direnç Mungan studied Molecular Biology and Genetics at İstanbul University  focusing on the Bionformatic Applications on various DNA forms and their potential  link to certain diseases. His interest on the Bioinformatics field led him to work with Assoc. Prof. Jens Allmer in İzmir Institute of Technology on proteomics and  effective database handling when analyzing mass spectral data with database search  algorithms. He worked a year with Prof. Dr. Anne Frary on transcriptomic analysis of Pucinellia Distans when subjected to multiple chemicals and genome assembly for SSR detection of various plants. Since September 2018 he is working as a PhD candidate to improve genome mining tools for natural product discovery.


Shrikant Mantri


After completing his B.Pharmacy studies from University of Pune, Shrikant chose to pursue Master's in Bioinformatics at Indian Institute of Information Technology Allahabad, mainly to gain skills in computing and informatics to explore the biological big-data genomics questions and learn more about computer aided drug designing. Subsequently during his research stints at National Botanical Research Institute and National Agri-Food Biotechnology Institute, Shrikant has contributed in developing supercomputing enabled softwares and databases for accelerating plant genomics research and has collaborated with many groups interested in designing nutritionally improved crops. In ZiemertLab since October 2018, Shrikant is developing new software tools, pipelines and databases to facilitate the natural product discovery using metagenomics big-data. 


Franziska Höhn

Franziska Höhn studied food sciences and biotechnology at the University of Hohenheim. She finished her Bachelor´s degree on the field of food microbiology and hygiene. Interested in microorganisms, she started her Master´s degree in microbiology at the University of  Tübingen. In October 2019, Franziska finished her Master thesis in the field of screening metagenomic libraries for natural products in the group of Applied Natural Products Genome Mining. Fascinated by the great opportunities in natural product research, she stayed in the group as a PhD student. In a cooperation project with the AG Brötz-Oesterhelt and the Kemen group, Franziska investigates the role of natural products in shaping microbial communities. As a model system, she uses a bacterial synthetic community from Arabidopsis thaliana (Kemen group). Her work aims to increase the knowledge of natural product based interactions in nature and helps to identify members important for plant health and disease prevention.


Athina Gavriilidou

Athina Gavriilidou studied Biology at the Aristotle University of Thessaloniki, during which she became interested in the application of informatics tools that further biological goals. She completed a Masters Degree in Bioinformatics at the Eberhard Karls University of Tuebingen. At that time she was hired as a student assistant in ZiemertLab, where she wrote her Master Thesis on the Natural Product potential and diversity within the bacterial kingdom. Since February 2020 Athina is working as a PhD student, researching the evolution of glycopeptide biosynthetic gene clusters and their interaction with bacterial primary metabolism.


Bita Pourmohsenin

Bita Pourmohsenin got her Bachelor’s and Master’s degree in Computer Science from Amirkabir University of Technology (Tehran Polytechnic), during which she found her interest in the Application of computational methods in Bioinformatics. As her Master’s thesis, she worked on developing an algorithm for Phylogenetic Tree Reconstruction based on Clustering.Finding her passion in Bioinformatics, she decided to pursue a PhD in the field. She joined the Ziemertlab team in February 2020, as a PhD student. She is currently working on exploring the potential of environmental metagenomic data. 

Master Students

Patrick Weiss


Patrick Weiß studied biology at the University of Tübingen. He finished his Bachelor’s degree on the field of evolution and ecology, where he worked on the filarial parasite Onchocerca ochengi. Interested in microorganisms, he continued his studies in Tübingen with starting his Master’s degree in mircobiology at the University of Tübingen.


Monica Daneliuc

Monica Daneliuc completed her bachelor’s degree in biochemistry at the Eberhard Karls University of Tübingen. Since her bachelor studies she was interested in applying informatics in biochemistry. Her bachelor thesis focused on the development of a graph database connector in Python. That is why she chose to continue her studies with a master’s in bioinformatics, also at the University of Tübingen. She is currently writing her master thesis on the topic of identifying uncultured secondary metabolite producers from metagenome data at Prof. Nadine Ziemert’s group.

Davide Paccagnella

Davide studied biology at the University of Tübingen. During his bachelor thesis he worked with cyanobacteria, where he looked at the mechanism of intercellular communication of Anabaena sp. PCC 7120 and how this mechanism is affected by intracellular pH alterations. Because of his interest in microbiology he continued his studies with a master in microbiology. For his master thesis he is working on different actinomycetes clusters obtained trough genome mining to identify secondary metabolites with a potential therapeutic application.


Ziemertlab Alumni

  • Mohammad Alanjary, Ph.D Student
  • Helena Sales-Ortells, Postdoc
  • Michelle Schorn, UCSD visiting student
  • Maryam Elfeki, UIC visiting student
  • Kyra Geyer, Master student
  • Frauke Adam, Master Student
  • Katharina Steinke, Master Student
  • Anastasia Leonova, Master Student