Animal and plant microbiome functions can be modulated, and thereby optimized, for sustainable food production. However, the outcome, i.e., the microbial response, can vary greatly depending on (e.g.)Animal and plant microbiome functions can be modulated, and thereby optimized, for sustainable food production. However, the outcome, i.e., the microbial response, can vary greatly depending on (e.g.) the genetic background and developmental stage of the host, and the farming environment. The interactions between the biological process of the host and their microbiome are still only superficially understood, even though microbial interventions have been used for years. This incomplete understanding means that new attempts to improve microbiome functions are both inefficient and costly, and unlikely to hit upon the optimal solutions. An approach that recognizes the intimate biological interactions between host genome and microbiome functions holds the potential to greatly reduce cost and improve the outcome. To that end, FindingPheno will develop a holistic statistical framework to decipher biomolecular interactions between host and microbiome by combining biological knowledge and state-of-the-art statistical methods: structural causal modelling, variable selection, dimensionality reduction and feature detection. We will then apply the framework to case studies from actual food production systems, using a unique multi-omics data set from three biological systems – chicken, salmon and maize – derived from ongoing research projects. In addition, we demonstrate the utility of the framework to obtain biological insights from publicly available data sets from tomato and bees. We expect to show how to improve the effectiveness of microbiome interventions in sustainable food production, and simultaneously, we will offer avenues for quick and easy application of this new approach to other relevant biotechnology-based industries, e.g. enzyme production and fermentation.

Reducing lead times of new medicinal drugs to the market by reducing process development and clinical testing timeframes is a critical driver in increasing European (bio)pharmaceutical industry competitiveness. Despite new therapeutic principles (e.g. the use of pluripotent stem cells, regenerative medicine and treatments based on personalised medicine or biosimilars) or regulatory initiatives to enable more efficient production, such as Quality by design (QbD) with associated Process Analytical Technology (PAT) tools , the slow progress in the development of new bioactive compounds still limits the availability of cheap and effective medicines. In addition, the competitiveness of European (bio)pharma industry is impacted by the unavailability of suitably trained personnel. Fundamental changes in the education of scientists have to be realised to address the need for changes in the traditional ‘big pharma’ business model and the focus on ‘translational medicine – more early stage clinical trials with patients, more external innovation and more collaboration’ . These changes in education should be based on combining cutting-edge science from the early stage of product development through to manufacturing with innovation and entrepreneurship as an integral part of the training. The Rapid Bioprocess Development ITN, employing 15 ESRs, brings together industrialist and academic experts with its main aim to address this critical need by developing an effective training framework in rapid development of novel bioactive molecules from the very early stages of potency and efficacy testing to the biomanufacturing process characterisation and effective monitoring. The main focus of the research is on oncology related proteins and recombinant proteins to be used in diabetes treatment, although the resulting monitoring and modelling methods will be applicable to other bioactive molecule process development as demonstrated by validation on a range of relevant bioactives.

Streptococcus suis is an endemic porcine disease causing causing significant economic losses to the pork meat production industry in all countries where pigs are reared on a large scale. In some countries S. suis is the primary cause of mortality and morbidity in young pigs and the most frequent reason to prescribe antibiotics of the amino-penicillin group as a preventative measure. S. suis is also a zoonotic pathogen of humans and infections reported worldwide has increased significantly in the past years. Within S. suis many different types (serotypes, genotypes, pathotypes) exist causing problems in the development of control strategies targeting all types. Asymptomatic carriage in adult pigs is common and combined with a lack of knowledge on the host-pathogen-environment interactions, are the main reasons for failure to control the endemic nature of this pathogen. The project outputs will impact on on understanding host-pathogen-environment interactions of S. suis infections through the genome sequencing of 1200-1500 S. suis isolates from representative geographic areas of the major pork producing countries and performing genome-wide-association studies with invasive disease and asymptomatic carriage. New diagnostic methods will be developed for global monitoring of infection risk and tested on case-farms. Epidemiology studies will determine risk factors for invasive S. suis disease, including the role of co-infections, and for the first time properly assess the dynamics of the disease on a representative farm. We will increase our understanding of the virulence mechanisms involved in pathogenesis including interactions of S. suis with the innate immune system. The project outputs will strengthen the evidence base for prevention and control strategies through testing of novel conserved vaccine antigens in pigs and prevention strategies based on manipulation of the microbiota and stimulation and maturation of the innate immune system.

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.