The research group for Environmental Biotechnology, supervised by Prof. Lars Angenent, has accompanied our team during the whole iGEM year, with two doctoral students, Sarah Schulz and Patrick Schweizer, being our instructors and Dr. Bastian Mollitor, our PI. Pengfei Xia’s expertise in synthetic biology was necessary for the design of the CRISPR/Cas3 based kill switch (Project/Kill Switch). Bastian, Sarah and Patrick are experts in biotechnology and working with anaerobic conditions. This was a requirement to our Nissle characterisation and the generation of our RNA Sequencing samples (Project/Nissle). We also had the chance to present our project and iGEM in general at the microbiome supergroup talk at the Max-Planck-Institute in Tübingen. There we got the information about a group in Cornell, USA which is working on a similar project. In general we got positive feedback on our project and future plans.

Dr. Anette Christ, from the Institute of Innate Immunity in Bonn (Group Prof. Eike Latz), is an expert in the influence of Western Lifestyle on Inflammation caused by diet and lifestyle. Moreover, she and her group are constantly following outreach programmes in nutrition and Diabetes prevention. Through her data, we decided to add Clostridium Difficile supernatant to our Nissle characterisation, as it is harbouring inflammatory potential. Moreover, our knowledge and planning of our communication strategy was based on literature and data provided by Dr. Christ.

Prof. Müller, acting director of IDO (Institute for Diabetes and Obesity) of the Helmholtz Institute Munich is researching Diabetes Mellitus. When proposing our ideas to him, he pointed us towards several weak-points of our initial idea: i) the fast degradation of GLP-1 by DPP-IV and other peptidases and ii) the low bioavailability of our therapeutic, if it is not actively brought into the circulatory system. Consequently, we researched alternatives of GLP-1, which led us to the more stable Exendin-4. To solve the second concern, we fused a cell penetrating peptide with Exendin-4 in order to pass the intestinal epithelium.

Prof.Dr. Andreas Fritsche is the deputy director of the Insitute for Diabetes Research and Metabolic Diseases at the University Clinic Tuebingen. We met with Prof. Fritsche to get a clinical opinion on our project. He made us aware of the potential of the outlook of our product as obesity treatment (Project/Outlook) and that we would have to work against the negative connotation of GMOs as unhealthy and unnatural. Prof. Fritsche also gave a gross estimate that about a third of his patients may be willing to test a new therapeutic strategy, if it was safe.

Consequently, we designed a survey to gather information on the public’s perception on GMOs and Diabetes Mellitus (Human Practices/Survey). The aim of the survey was to find out whether the public would be willing to use a GMO-containing therapeutic, while analysing if further education about GMOs is required for higher acceptance.

With Dr. Hecker, Head of the technology transfer department at the University of Tuebingen, we discussed strategies for founding a start-up, intellectual property protection under iGEM’s Creative Commons License and how a biotechnological start-up by students could be competitive (Human Practices/Entrepreneurship). Dr. Hecker hinted us towards open innovation and providing our CRISPR/Cas 3 system as a service for partners to allow for biocontainment of their projects. This would help us finance a business through the stages of preclinical testing. Furthermore, we looked into the world-wide regulatory barrier of entering the market with an engineered pharmaceutical, in order to identify a market on which we could initially place our product. We finally decided on Egypt.

Through the discussion with Dr. Lisa Maier, Group leader at the Interfaculty Institute of Microbiology and Infection Medicine, we were able to thoughtfully design our RNA-Seq experiments and choose appropriate parameters to investigate (Project/Nissle). She also pointed us toward the importance of the gut microbiome composition which finally led to our metabolic modelling approach (Project/Model). Moreover, Dr. Maier, helped us identify five bacterial species for our anaerobic growth experiments.

At Synovo, a drug discovery company focusing on inflammation and innate immune processes, we discussed the pharmacology of Exendin-4. Additionally, the synovo team provided us with their experience about the implications of founding a start-up within the biotechnological sector (Human Practices/Entrepreneurship). We discussed the drug admission process up to clinical trials and entry to the market of our product. Moreover, we in detail looked into the costs of keeping a laboratory running at the different stages of production and testing, including the maintenance of quality and safety of our product.

Prof. Dr. Andreas Dräger, Assistant Professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, is an expert in metabolic modeling. He introduced CarveMe as a novel tool for the creation of metabolic models to us and gave us very valuable pointers for our subsequent modelling approaches.

Inspired by Advanced Transcriptomics lectures by Prof. Dr. Kay Nieselt, Group leader of Integrative Transcriptomics, we decided to characterize the transcriptome of E. coli Nissle 1917 under various stress conditions.

To further refine our modelling approaches, we met with our long time supporter Prof. Dr. Oliver Kohlbacher, Professor for Applied Bioinformatics, of the Applied Bioinformatics Group at the University of Tübingen. We discussed our RNA-Seq experimental design with respect to an E. coli Nissle characterization, evaluation of the safety of our tool, as well as the viability of our regulation system under different conditions (Project/Nissle).

For his doctoral degree Dr. Stefan Gammel has researched the cultural aspects of ethical discussions within the area of nanotechnology. He helped us with the ethical evaluation of the project of iGEM TAU (People/Collaborations). Furthermore he provided valuable insights into the ethics guidelines of iGEM which helped us to think further about our own obligations and led us to a more generalized approach to educational outreach where we also covered the general public (Human Practices/Overview).

Dr. Angel Angelov, Lab Manager at the Microbial Genomics and Metagenomics facility of the NCCT (NGS Competence Center Tübingen), is one of our experts in RNA sequencing at the core facility in Tuebingen. Angel and his colleagues (Christina Engesser, Manuela Löffler), have great expertise in isolating and preparing RNA, allowing them to ensure our RNA Sequencing experiments can be successfully completed. Since after our first two trials of RNA isolation, rRNA depletion and RNA-Seq library preparation did not go as well as expected, we discussed our approaches, kits and possible sources of mistakes with Dr. Angel Angelov and his colleagues. The third and final library preparation was then good enough for sequencing.

Dr. Vladimir Benes, Head of the Genomics Core Facility of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is an expert in transcriptomics, providing us with the sequencing of our RNA. His expertise with genomics, transcriptomics and more specifically RNA-Seq specifically, greatly shaped our RNA-Seq experimental design. It was after intense and fruitful discussions with Dr. Vladimir Benes that we came to the conclusion that we should also include anaerobic conditions to reflect the common environment of probiotics.

At the EMBL we met with Dr. Daniel Machado, Computational Biologist at EMBL and the developer of a tool for metabolic model reconstruction (CarveMe), to get tips to further improve our generated model. DIscussing our approach with him led to the decision to further investigate the growth of E. coli Nissle in presence of different media (Project/Nissle https://2019.igem.org/Team:Tuebingen/Nissle). In addition, he further inspired our modeling, by explaining and introducing Smetana, a tool which can be used to investigate interactions in microbial communities (Project/Model).

Together with Dr. Schibel and Dr. Walderich, both safety officials of the University of Tübingen and the Max Planck Institute Tübingen, we evaluated the biological safety of our cell penetrating peptides (Safety). Together, we identified the work with cell penetrating peptides as Biosafety Level 1 work.