Periodic Reporting for period 2 - e.Biofilm (Creation of a group of Excellence on Engineered Biofilms)
Reporting period: 2024-07-01 to 2025-10-31
Biofilms are interactive communities of interface-associated microbial cells, enclosed in a matrix of extracellular polymeric substances. Biofilms are ubiquitous both in nature and human-built environments, and impact clinical infections, environmental sustainability, and industrial processes. Consequently, biofilms are central to many of the domains of research and innovation identified in the Treaty on the Functioning of the European Union, and exert considerable economic pressure across healthcare, environment, and industry. As our fundamental knowledge of biofilm increases, so does the need for guidance on how to regulate biocides, medical devices, and processes designed to control, kill, remove, or exploit biofilms. The main objective of this proposal project is to establish a Group of Excellence on Engineered Biofilms at the Faculty of Engineering of the University of Porto (UPorto). Worldwide impact requires not only excellence in the stated biofilm research foci, but also a technology transfer program that promotes innovation, a thriving educational and training program, and communication and dissemination strategies that establish links with the scientific community, other relevant stakeholders, and the public. To achieve these objectives, e.Biofilm will build on existing expertise from the ERA Chair holder Darla Goeres from the Center for Biofilm Engineering of Montana State University (MSU). The main goals of e.Biofilm are: 1) establish better links between research and innovation to shorten the path from fundamental research on biofilms to industrial and clinical solutions; 2) serve as a training and networking hub for young students and professionals, with a profound, yet wide, understanding of the field of biofilms in healthcare and industry, and the tools/knowledge needed to develop biofilm-related technologies; 3) simultaneously inform the general public and other relevant stakeholders in the European Research Area (ERA) about innovative technologies that enable biofilms to be engineered in a reproducible way.
Significant progress was made towards creating a group of excellence:
-The e.Biofilm team has grown. New junior researchers with expertise in complementary research areas were added.
-Additional students have been recruited.
-The team participated in key conferences which enabled them to expand their network, promote their research and lay the ground work for future collaborations.
-An EU COST Action CA23152 was funded to support the promotion of tools for regulatory decision making and network expansion.
-Research was published in open access peer reviewed journals.
-Funding from FCT (Portuguese funding agency) was secured to leverage the e.Biofilm project funding and support PhD students after the lifetime of the e.Biofilm project.
-Portuguese Norte2030 funding was secured. Funding is being used to support additional students, purchase equipment, and provides support for exploitation and technology transfer.
-Two training schools and two scientific workshops were completed.
-15 scientific seminars were given by visiting researchers from across the EU, UK, and US.
-Meetings were held with the advisory board and their feedback incorporated.
-ALiCE (Associate Laboratory in Chemical Engineering) and DEQ (Chemical Engineering Department) continued to provide in kind strategic fundings to acquire state of the art research equipment.
-Established secondments between e.Biofilm researchers and academic collaborators.
-Implemented a strategy to engage with industry and initiated contacts to promote innovation with the purpose of registering projects with biofilm claims.
-The e.Biofilm team has grown. New junior researchers with expertise in complementary research areas were added.
-Additional students have been recruited.
-The team participated in key conferences which enabled them to expand their network, promote their research and lay the ground work for future collaborations.
-An EU COST Action CA23152 was funded to support the promotion of tools for regulatory decision making and network expansion.
-Research was published in open access peer reviewed journals.
-Funding from FCT (Portuguese funding agency) was secured to leverage the e.Biofilm project funding and support PhD students after the lifetime of the e.Biofilm project.
-Portuguese Norte2030 funding was secured. Funding is being used to support additional students, purchase equipment, and provides support for exploitation and technology transfer.
-Two training schools and two scientific workshops were completed.
-15 scientific seminars were given by visiting researchers from across the EU, UK, and US.
-Meetings were held with the advisory board and their feedback incorporated.
-ALiCE (Associate Laboratory in Chemical Engineering) and DEQ (Chemical Engineering Department) continued to provide in kind strategic fundings to acquire state of the art research equipment.
-Established secondments between e.Biofilm researchers and academic collaborators.
-Implemented a strategy to engage with industry and initiated contacts to promote innovation with the purpose of registering projects with biofilm claims.
e.Biofilm aims to advance biofilm research using imaging and molecular characterization by using various technologies (e.g. bioreactors, molecular biology, microscopy, statistics, and computational simulation) to gain a deeper understanding of the biogeography of biofilms. The project is focused on two case studies: industrial systems (Focus Area 1, FA1) and chronic wound infection (Focus Area 2, FA2). Imaging analysis tools will be developed to effectively discriminate between bacteria and matrix components in multi-species biofilms generated by FA1 and FA2 and accurately record their spatial distribution. The resulting images will be securely stored in a database that incorporates the 3D aspects of the method (Focus Area 3, FA3). This innovative approach is designed to characterize multiple components, ultimately leading to more meaningful, statistically relevant data using computational models (Focus Area 4, FA4).
Ongoing research is being carried out by the PhD students. To date, the research has resulted in the development of a spatial transcriptomic method, using multiplex mRNA PNA-FISH, providing essential data on gene expression in individual Legionella pneumophila cells, both in the planktonic and sessile states, while also recording functionality and spatial information. In addition, progress has been made in refining protocols to image the matrix and correlate the images to the mechanical properties of a Klebsiella pneumoniae biofilm. FA2 is focused on studying the spatial distribution of Pseudomonas aeruginosa / Staphylococcus aureus biofilms in a chronic wound model. A repeatable model has been developed, and research is ongoing into how the spatial arrangement responds to changes in key nutrients over time. FA3 has completed a comparative analysis of the state-of-the-art segmentation tools for 3D confocal microscopy images to determine which provides the most accurate output. The development of a database to log the images is in the progress, with the most important meta data identified to comply with the FAIR principles. A collaboration with the University of Vigo, Spain, has been established to support agent-based modeling of biofilms.
Ongoing research is being carried out by the PhD students. To date, the research has resulted in the development of a spatial transcriptomic method, using multiplex mRNA PNA-FISH, providing essential data on gene expression in individual Legionella pneumophila cells, both in the planktonic and sessile states, while also recording functionality and spatial information. In addition, progress has been made in refining protocols to image the matrix and correlate the images to the mechanical properties of a Klebsiella pneumoniae biofilm. FA2 is focused on studying the spatial distribution of Pseudomonas aeruginosa / Staphylococcus aureus biofilms in a chronic wound model. A repeatable model has been developed, and research is ongoing into how the spatial arrangement responds to changes in key nutrients over time. FA3 has completed a comparative analysis of the state-of-the-art segmentation tools for 3D confocal microscopy images to determine which provides the most accurate output. The development of a database to log the images is in the progress, with the most important meta data identified to comply with the FAIR principles. A collaboration with the University of Vigo, Spain, has been established to support agent-based modeling of biofilms.