BestTreat fosters education of ESRs in a project to uncover microbiome signatures for risk prediction and monitoring of NAFLD and to contribute to the development of therapeutic treatments based on metabolically beneficial microbial consortia. It trains 15 ESRs at world-leading academic institutions and companies, thus forming strong interdisciplinary links between industry, life and medical sciences, and end-users. BestTreat aims to train a new generation of highly qualified ESRs with entrepreneurial competencies in modern Life Sciences through state-of-the-art research projects. The projects focus on the identification and functional characterization of microbial consortia that contribute to metabolic control, and the application of this knowledge to develop novel leads for drug discovery and therapies for NAFLD. The new field on microbiome based therapeutics requires highly skilled scientists with interdisciplinary knowledge on medicine, systems biology and computer science, as well as hands-on experience with several types of tissue samples and model organisms that can optimally translate their research findings into sustainable improvements in clinical practice. BestTreat overcomes current barriers by establishing a strong, multidisciplinary and inter-sectoral training network, developing technologies tailored to solve key questions in human metabolism, microbiology and bioinformatics. The BestTreat programme will exploit recent developments in high-throughput and genome-wide screening technologies, combine these with modern molecular cell biology and systems biology approaches and ultimately translate the data into new leads for the discovery of live biotherapeutics. This specific cross-disciplinary training program will educate young scientists to the next level needed to advance this research field for the upcoming decennium. The training programme will be complemented with a complete set of transferable skills.

Microbiota medicine is the new frontier in human health. The human gastrointestinal tract is home to trillions of microbes. Under normal conditions, these microbial communities drive physiological and homeostatic functions in the host; when altered, they can lead to severe disorders. With an increasingly recognized role in health and disease, the gut microbiota offers promising therapeutic and diagnostic potential to tackle various pathologies (incl. metabolic, neurological, and cardiovascular disorders). Its full clinical potential remains largely unrealized though, mostly due to the lack of critical mass capable of integrating the multiple scientific and translational dimensions of microbiota medicine. Grounded on a team of 180leading researchers and entrepreneurs from across 12 countries and dispersed disciplines (biological big data analytics, systems and synthetic biology, experimental and translational medicine), MiCCrobioTAckle will train 12 Doctoral Candidates (DCs) with the much-needed cross-disciplinary and -sectoral expertise to advance microbiota medicine. As course-setting disease, the DCs will focus on cancer cachexia (CC). CC is an excellent model to study the host-microbiota axis in the context of metabolic diseases and represents the paradigm of a devastating condition in urgent need of new and more efficient means of clinical management. Along MiCCrobioTAckle, the 12 high-calibre DCs will foster new discoveries with impact on CC, while driving scientific and technological progress in microbiota medicine in its broadest scope. By training the next generation of researchers with out-of-the-box thinking and an entrepreneurial mindset in microbiota medicine, MiCCrobioTAckle will safeguard the EU leadership in this vanguard and imperative biotech/pharma segment, while paving the way for the development of novel gut microbiota insights and tools to tackle multiple diseases with foreseeable impact on the well-being of billions of citizens worldwide.

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).

Fungal infections have a major impact on human health, infecting about 2 billion people and killing more people each year than malaria or breast cancer. In particular, Candida species impose a high clinical and economic burden upon the European population. They frequently cause fatal hospital-acquired bloodstream infections. They also cause oral thrush and vaginitis. Most women have suffered an episode of vulvovaginal candidiasis, with ~8% enduring recurrent infections. The initiation and severity of a Candida infection depends on an intricate interplay between the infecting fungal strain and the individual’s immune status and microbiota, all of which can display significant variability. Therefore, for the first time, FunHoMic integrates experts in fungal pathogenesis, immunology, microbial ecology and ‘omics technologies to train 13 Early Stage Researchers (ESRs) who will define and exploit this Fungal-Host-Microbiota interplay to identify novel biomarkers (fungal or host genetic polymorphisms, microbiota profiles, metabolites or immune markers) for the stratification of a patient’s risk of serious fungal infection. This will pave the way for precision medicine in patient management through preventive or therapeutic interventions using antifungals, immune modulators or Live Biotherapeutic Products (LBPs). FunHoMic ESRs will gain broad interdisciplinary skills plus a translational mindset through our integrated, inter-sectoral training program. This will allow Europe to remain at the forefront of translational research in the field of medical mycology. To achieve this vision FunHoMic unites academic partners from France, Germany, The Netherlands, Switzerland, Spain and UK, a French Technology Research Institute with cutting-edge ‘omics technology platforms and three SMEs from The Netherlands, Belgium and France that bring unrivalled organ-on-chip and gastro-intestinal tract simulation technologies and expertise in the development and exploitation of innovative LBPs.