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Microbial Communities in Biomedical and Environmental Areas, and Systems Biology

Periodic Reporting for period 2 - MiCoBion (Microbial Communities in Biomedical and Environmental Areas, and Systems Biology)

Reporting period: 2019-12-01 to 2022-11-30

Microbial communities (microbiomes) have a major impact on humans, animals, and ecological niches. The main goal of MiCoBion was to strengthen scientific excellence and innovation capacity at Charles University and its Biotechnology and Biomedicine Center (CUNI-BIOCEV) via collaboration with Catholic University of Leuven (KUL), European Molecular Biology Laboratory (EMBL), and University Paris Diderot-Institute Jacques Monod (UP-IJM) in the field of high throughput molecular profiling of biological systems that will foster innovative research of complex microbial communities and their impact on health and environment. The research of complex microbial communities is based on three pillars: excellent knowledge in microbiology, high throughput technologies that generate voluminous datasets, and computation of these "big data". The strength of CUNI is an excellent knowledge of microbial systems important for human and animal health, and environmental issues. Weakness is the research capacity in analysis of "big data", and limited experience in innovative research and technology transfer. Thus, twinning activities focused on promoting of knowledge and research capacity at CUNI in the defined area of bioinformatics, cutting-edge multiomics technologies, and establishing a pipeline from excellent basic research to high value-added applications. Activities included the exchange of scientists, joint supervision of young scientists, organization of seminars and lectures, participation in EMBL and CUNI courses, and dissemination in the scientific community, industries, and the public.
WP1 focused on the increase of theoretical knowledge via the participation of PhD students and junior scientists in courses at EMBL and KUL (279 young researchers and students trained), it deals with the organization of summer school at CUNI (11 young researchers participated) and facilitated joint supervision of 11 students and young researchers.
WP2 coordinated short stays of PIs to elaborate the research plan specified for each collaborative team in the Scientific strategy. Then, WP2 coordinated visits of 23 PhD students and young researchers (56 weeks) to get practical experience with technologies in the area of DNA/RNA sequencing using single molecule approach, comparative proteomics, metabolomics, and polyomics). Knowledge of how to stimulate the application of research results and boost technology transfer was acquired in intensive training of CUNI technology transfer office experts at the partner sites.
WP3 focused on the enhancement of networking activities via invitations of experts in microbial community research, related technologies, and innovation to CUNI. Through WP3 activities 12 experts from partner institutions delivered lectures to more than 309 participants on the most recent advances in the field of microbiome research, and the essential and advanced approaches in the analyses and integration of big data. Furthermore, they held discussions with teams from CUNI and individual consultations with students. Moreover, lectures were given by 18 world-renowned experts on the topics of the interactions of yeasts, protists, and viruses with the other members of human and animal microbiomes.
WP4 organized workshops for training in top-notch technologies, intellectual research approaches, networking among experts, and strategies in innovative research and technology transfer. 16 young researchers gained theoretical and practical knowledge in mass spectrometry-based proteomics, 25 researchers gained a complex insight into the problematic of yeast aging, metabolic reprogramming, cell differentiation and adaptation, 25 researchers learned how to analyse datasets from mouse microbiomes, 120 researchers participated to a conference which showcased the latest trends in the area of microbial communities and during which outcomes of MiCoBion-based research collaborations were presented. MiCoBion was presented in three science-to-business events, showcasing its expertise and readiness to collaborate with industry, as exemplified by several established but also novel collaborations.

The objective of dissemination was to assure that the results of the project would be disseminated to the European research and industrial community, targeting all important stakeholders. Throughout the project, a maintained a steady presence in this field, both online and offline activities. With the return of in-person events, dissemination efforts of all partners have increased towards the end of the project period.
One of the main visions of the project and its overall impact is the fostering excellence of research and innovation at CUNI in the field of microbial communities and systems microbiology, which will be translated into applications such as discovery of new pathogens (viruses), identification of new biomarkers for diseases, factors for immunity modulation, candidates for vaccines, and new drug targets. The following progress has been reached:
• Strengthened knowledge and implementation of new approaches in high-throughput technology applications (genomics, transcriptomics, proteomics, metabolomics) for microbiota analysis and systems biology.
• Strengthened knowledge and implementation of new tools for big data computing with a focus on research of challenging microbial communities.
• Enhancement of innovative research.
The research excellence has been reinforced by setting up 8 interdisciplinary research teams which applied the knowledge and skills learned in Twinning activities and delivered 33 publications in top peer-reviewed journals. This constitutes more than a three-fold increase. The raised excellence resulted also in enhanced collaborations with foreign research institutions, resulting, among others, in the successful acquisition of a new project under EU4Health program HERA that will establish international collaborations in preparedness and response to cross-border health threats (20 institutions from 15 countries).
The expertise of CUNI in innovative research and technology transfer has been raised thanks to intensive training of TTO staff at partner sites. Innovation-focused initiatives resulted in the enhanced database of industrial connections and 3 new formalized partnerships with industrial partners.

Thus, CUNI responds to pressing societal needs and supports the applicability of research outcomes. Through its activities, MiCoBion impacted the regional, national as well as European society:
• Increased international visibility of Vestec and the STAR Region through hosting of foreign expert researchers during their short-term visits and lectures (WP3), workshops, and conferences (WP4)
• The motivation of elementary and high school students for further university studies in natural sciences through visits at schools and student visits at CUNI
• Communication activities (WP5) explaining the importance and economic and social benefits of research and development for the broad public (participation in events focused on public – e.g. BIOCEV days, articles in magazines, TV interviews).

Combined with other impacts, such as the enhanced curriculum of CUNI programmes in bioinformatics, enhanced activities towards elementary and secondary school students, and an extended list of specialized methods offered by CUNI labs, the project has been a great success in delivering positive impacts to CUNI as well as foreign partners.