In many bioprocesses a broad bioproduct portfolio can currently only be obtained when microorganisms can access oxygen as an electron acceptor. For numerous target substances, however, oxygen is detrimental to product stability and the bioprocess operation. The central aim of e-MICROBe is to innately couple microbial metabolism and electrochemistry via a self-secreted soluble electron mediator to achieve efficient oxygen independent energy metabolism and to directly steer and control metabolism and product formation. This will require creating entirely new physiological traits for production and utilization of redox mediators to generate cellular energy. Thereby, mediators can either act as electron discharge shuttle to enable electro-respiration at an anode or they are employed as inorganic energy donor to deliver electrons from a cathode into the metabolism. We will clarify the underlying reaction pathways in known environmental microorganisms and re-engineer the energy metabolism of common biotech hosts. Thereby, we will switch cellular energy generation from aerobic respiration to anaerobic anodic electro-respiration or from hydrogen consumption as autotrophic electron donor to cathodic electron consumption. The latter process will provide a mechanism to store electrical energy in microbial products. For a new level of in situ insight into microbial energy metabolism, a novel micro-scale bioelectrochemical reactor coupled to microscopic observation and high performance analysis will be developed. With this technique two fundamental concepts for future mediator-based bioprocesses will be evaluated: An all-in-one strategy where one cell is generating the mediators and the targeted product as well as a co-culture system, whereby one cell produces the mediators and a partner cell utilizes them for electro-respiration and product formation. This concept will lay the foundation for a plug-and-play exchange of biotech strains in a mediator-producing co-culture system.

T helper cells represent a heterogeneous population of immune cells that are critical for host defense and, if dysregulated, for pathologies such as autoimmunity and allergy. T cell responses take place in peripheral tissues. Yet, insights into their identity and regulation stem almost exclusively from investigations of circulating blood, which comprises only 2% of the total human T cell population. Accordingly, current immunomodulatory drugs act systemically, but lack tissue specificity. Despite progress in the temporary suppression of chronic inflammatory diseases, they still fail to be curative. This project aims to address this unmet medical need by generating fundamental insights into the dynamic compartmentalisation of human tissue resident T helper cells across space and time. I have established a surgical patient cohort for the collection of multi-organ tissue samples and a cohort of patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) that enables tracking T cell tissue entry and exit over time in matched organs by single-cell chimerism analysis. Using multimodal state-of-the-art technologies and specialised high-throughput cell culture methodologies in these two unique patient cohorts, the project will dissect 1) the phenotypic, functional and transcriptional identity and molecular regulation of human resident T helper cells across tissues, 2) the compartmentalisation of their antigen specificities across tissues, 3) the dynamics of tissue entry, persistence and exit for distinct T helper cell types in space and time, and will then 4) exploit chimeric host/donor T cell-tracking to gain novel insights into the cellular and molecular pathways underlying graft-versus-host disease. Overall, ORGANise-T will establish first-of-its-kind insights into the spatio-temporal dynamic organisation of human T cell immunity in tissues. This will bring the next generation of immunotherapies to the level of tissue specificity.

Anaerobic bacteria, a group of microorganisms that thrive in the absence of oxygen, have a significant impact on the quality of life on Earth. They play a crucial role in biotechnology and are essential components of the gut microbiota. As such, they are of tremendous importance for human, animal, and environmental health. On the other hand, certain anaerobes can be life-threatening pathogens. In light of this, there is an urgent need for a deeper understanding of the specialized metabolites of anaerobes, which could function as chemical mediators, virulence factors, and antibiotics. Although genome analyses indicate that anaerobic bacteria hold an enormous potential for producing structurally unique compounds, biosynthetic gene clusters are typically downregulated or silent under laboratory conditions. Synthetic biology approaches to unearth these cryptic pathways have been hampered by the lack of universal activation strategies, the cumbersome genetic tractability of anaerobes, and the incompatibility of standard expression systems with the oxygen-sensitive biosynthetic enzymes. The AnoxyGen project seeks to unearth the vast structural wealth of natural products from the anaerobic world and leverage their unique biosynthetic machinery using a highly versatile anaerobic expression platform. This ambitious initiative comprises four work packages aimed at refining synthetic biology tools, creating gain-of-function anaerobes, discovering novel drug candidates and virulence factors, and engineering biosynthetic pathways to create metabolic diversity. By achieving these objectives, AnoxyGen will grant a comprehensive overview on specialized metabolites and biocatalysts of anaerobes, which have great translational value for medicine, ecology, and biotechnology. In addition to providing valuable methods and tools to the scientific community, this project has the potential to bring significant benefits for the health and well-being of people, animals, and the environment.

FUNBIT aims to enhance the discovery rate of natural products applying a multidisciplinary workflow guided by Imaging MS. Microbial genetics predict that the natural products we have discovered so far are only the tip of the iceberg, thus we may be missing the antibiotics and biopesticides of the future. In fact, many natural compounds remain invisible under standard laboratory conditions, but their biosynthesis can be triggered by re-establishing the structure of their native community in multi-microbial co-cultures. Thus, hidden natural products that enable microbes to communicate and compete with each other can be revealed. However, microbial interkingdom partnerships such as fungi-bacterial microbial interactions are still in general poorly explored. The detection of cryptic natural products from microorganisms is a major challenge because many of them are produced in small quantities, in a specific area and during a short period of time. The emerging technology of Imaging Mass Spectrometry can be the best candidate to investigate multi-partner microbial interactions in their native ecological environment, and find the natural products involved in their cross-talk. FUNBIT aims to speed up the rate of natural product discovery (especially polyketides, and lipopeptides, since many antibiotics fall into these groups) by integrating Imaging MS with High Resolution MS, spatial statistics and molecular network analysis. We will focus on fungi-bacterial partnerships involved in important agricultural infections, such as root diseases. These microorganisms are safer to handle, but the discovered antibiotics and antifungals will potentially target human pathogens. FUNBIT will be supervised by Prof. Christian Hertweck, who was awarded in 2015 with the Gottfried Wilhelm Leibniz Prize for his expertise in natural products. FUNBIT will be developed at the Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI) in Jena (Germany).