Periodic Reporting for period 3 - PROMICON (HARNESSING THE POWER OF NATURE THROUGH PRODUCTIVE MICROBIAL CONSORTIA IN BIOTECHNOLOGY – MEASURE, MODEL, MASTER)
Période du rapport: 2024-06-01 au 2025-05-31
Harnessing natural microbiome consortia for bioproducts offers a promising solution to major societal challenges, including sustainability, resource efficiency, and the shift to a bio-based economy. Compared to single-strain systems, consortia provide greater stability, metabolic flexibility, and efficiency in converting renewable resources into valuable compounds like biofuels and bioplastics. PROMICON aimed at understanding and replicating the function of naturally efficient microbiomes by developing synthetic or enriched communities with targeted traits. This was achieved through an integrated, multidisciplinary approach combining omics technologies, machine learning, bioreactor engineering, and systems biology. Advanced tools were developed to identify key functional roles—primary producers (farmers), converters (labourers), and stabilizers (balancers)—within microbiomes. This knowledge enabled both the top-down simplification of natural consortia for pigment, EPS, and PHA production, and the bottom-up design of synthetic consortia for butanol, hydrogen, and biopolyester synthesis. New reactor systems and downstream processes were established, supported by early life cycle assessment. Multi-omics and genetic engineering approaches improved performance and set the stage for future sustainable applications of microbiome-based technologies.
WP1 – Learning from Nature: Enabling Technologies
Throughout the project, all 9 deliverables and 5 milestones were achieved. A real-time microbial monitoring platform was established, integrating flow cytometry and hyperspectral imaging. A comprehensive omics-based analysis system—encompassing IC/HPLC-MS, NMR, and proteomics—was developed and integrated to assess microbial function. Predictive models using PLS regression and microbiome data mining tools were created. A physics-informed neural network (PINN) model was also developed to forecast microbiome dynamics. During the final reporting period, D1.3 on genome-scale modelling of chemotrophic and cyanobacteria-rich microbiomes was delivered. WP1 successfully applied a systems-level approach to investigate microbial community structure, function, and dynamics—laying the foundation for rational design and control of synthetic consortia.
WP2 – Natural Consortia for Learning and Production
All 3 deliverables and 3 milestones were completed. Natural microbiomes from diverse environments were collected, characterized, and screened for PHA and EPS production. Bioreactor-scale production was optimized, including the use of PINN models for enhanced yields. In RP3, D2.3 reported optimal conditions for PHA, PHB, and EPS production based on WP1 modelling. Experimental efforts focused on optimizing heterotrophic and cyanobacteria-enriched consortia for the co-production of PHB, EPS, and phycobiliproteins, demonstrating the potential of naturally enriched microbiomes for scalable bioproduct synthesis.
WP3 – Synthetic Consortia for Production
All 9 deliverables and 4 milestones were achieved. Engineered microbial strains (farmers, producers, stabilizers) were developed for the biosynthesis of compounds such as acetate, sucrose, butanol, and PHACOS. During RP3, a bottom-up approach enabled the design of simplified synthetic consortia with high selectivity and productivity for biofuels and bioplastics using CO2 and light. The successful extension to include antimicrobial PHACOS highlights the flexibility and impact of the synthetic biology tools developed.
WP4 – Reactor Concepts
Four deliverables and three milestones were met. Novel reactor systems, including multi-chamber photobioreactors and biofilm reactors, were designed to support high space-time yields and process stability for (photo)trophic microbiomes. RP3 saw the delivery of D4.4 on in situ biofilm analysis in a custom-built CBR. Innovations included continuous cultivation techniques, integrated process control, and real-time monitoring—addressing key barriers in industrial microbiome application.
WP5 – Exploitation
All 4 deliverables and 1 milestone were achieved. RP3 focused on impact assessment, with completion of PROMICON’s LCA, S-LCA, Techno-Economic Analysis, and the Exploitation and Business Strategy Plan. These covered market analysis, IP management, stakeholder engagement, and environmental and economic evaluation, supporting the future uptake and commercialization of PROMICON technologies.
WP6 – Dissemination and Communication
Five deliverables and three milestones were fulfilled. A strong project identity, website, branding materials, and communication strategy were established and updated. During RP3, PROMICON’s results were disseminated across audiences—scientific (via publications and data sharing), policy (via briefs and dedicated content), industry (via factsheets and videos), and society (via media, social platforms, and newsletters)—ensuring broad outreach and stakeholder engagement.
WP7 – Management and Coordination; WP8 – Ethics
Six deliverables were submitted, covering data management, project coordination, and ethics compliance. In the final phase, the management team organized the concluding annual meeting, an innovation workshop, and coordinated preparations for the final review.
Throughout the project, all 9 deliverables and 5 milestones were achieved. A real-time microbial monitoring platform was established, integrating flow cytometry and hyperspectral imaging. A comprehensive omics-based analysis system—encompassing IC/HPLC-MS, NMR, and proteomics—was developed and integrated to assess microbial function. Predictive models using PLS regression and microbiome data mining tools were created. A physics-informed neural network (PINN) model was also developed to forecast microbiome dynamics. During the final reporting period, D1.3 on genome-scale modelling of chemotrophic and cyanobacteria-rich microbiomes was delivered. WP1 successfully applied a systems-level approach to investigate microbial community structure, function, and dynamics—laying the foundation for rational design and control of synthetic consortia.
WP2 – Natural Consortia for Learning and Production
All 3 deliverables and 3 milestones were completed. Natural microbiomes from diverse environments were collected, characterized, and screened for PHA and EPS production. Bioreactor-scale production was optimized, including the use of PINN models for enhanced yields. In RP3, D2.3 reported optimal conditions for PHA, PHB, and EPS production based on WP1 modelling. Experimental efforts focused on optimizing heterotrophic and cyanobacteria-enriched consortia for the co-production of PHB, EPS, and phycobiliproteins, demonstrating the potential of naturally enriched microbiomes for scalable bioproduct synthesis.
WP3 – Synthetic Consortia for Production
All 9 deliverables and 4 milestones were achieved. Engineered microbial strains (farmers, producers, stabilizers) were developed for the biosynthesis of compounds such as acetate, sucrose, butanol, and PHACOS. During RP3, a bottom-up approach enabled the design of simplified synthetic consortia with high selectivity and productivity for biofuels and bioplastics using CO2 and light. The successful extension to include antimicrobial PHACOS highlights the flexibility and impact of the synthetic biology tools developed.
WP4 – Reactor Concepts
Four deliverables and three milestones were met. Novel reactor systems, including multi-chamber photobioreactors and biofilm reactors, were designed to support high space-time yields and process stability for (photo)trophic microbiomes. RP3 saw the delivery of D4.4 on in situ biofilm analysis in a custom-built CBR. Innovations included continuous cultivation techniques, integrated process control, and real-time monitoring—addressing key barriers in industrial microbiome application.
WP5 – Exploitation
All 4 deliverables and 1 milestone were achieved. RP3 focused on impact assessment, with completion of PROMICON’s LCA, S-LCA, Techno-Economic Analysis, and the Exploitation and Business Strategy Plan. These covered market analysis, IP management, stakeholder engagement, and environmental and economic evaluation, supporting the future uptake and commercialization of PROMICON technologies.
WP6 – Dissemination and Communication
Five deliverables and three milestones were fulfilled. A strong project identity, website, branding materials, and communication strategy were established and updated. During RP3, PROMICON’s results were disseminated across audiences—scientific (via publications and data sharing), policy (via briefs and dedicated content), industry (via factsheets and videos), and society (via media, social platforms, and newsletters)—ensuring broad outreach and stakeholder engagement.
WP7 – Management and Coordination; WP8 – Ethics
Six deliverables were submitted, covering data management, project coordination, and ethics compliance. In the final phase, the management team organized the concluding annual meeting, an innovation workshop, and coordinated preparations for the final review.
All milestones and deliverables have been completed on time, reflecting strong coordination and effective project execution. The project has fully met its objectives, advancing beyond the current state of the art by deepening our understanding and application of complex microbiome consortia in biotechnology. This progress enables more efficient and sustainable production of high-value bioproducts. To date, 31 scientific publications have been released, with more in preparation, supporting widespread knowledge dissemination and innovation.
The expected impacts outlined in section 2.1 of the DoA remain fully relevant and are being actively addressed. The project is raising awareness of microbiomes’ transformative potential, generating new insights into industrial microbiome functionality, and strengthening sustainability and innovation across the bio-based sector. It supports the development of scalable, competitive bio-based solutions, informs policy through preliminary findings and releasing 5 policy briefs, and fosters innovation through stakeholder collaboration and big data analytics. Engagement efforts are also helping to build a framework for systemic innovation and future uptake of results.
From a socio-economic perspective, the project promotes green, microbiome-based technologies that support the shift from fossil-based to bio-based production, reducing environmental impact and boosting industrial resilience. These innovations pave the way for new value chains and inclusive economic opportunities, particularly in underdeveloped regions.
Overall, the project has validated its scientific and technological approaches while laying a strong foundation for long-term socio-economic and environmental impact—reinforcing Europe’s leadership in a sustainable, microbiome-driven bioeconomy.
The expected impacts outlined in section 2.1 of the DoA remain fully relevant and are being actively addressed. The project is raising awareness of microbiomes’ transformative potential, generating new insights into industrial microbiome functionality, and strengthening sustainability and innovation across the bio-based sector. It supports the development of scalable, competitive bio-based solutions, informs policy through preliminary findings and releasing 5 policy briefs, and fosters innovation through stakeholder collaboration and big data analytics. Engagement efforts are also helping to build a framework for systemic innovation and future uptake of results.
From a socio-economic perspective, the project promotes green, microbiome-based technologies that support the shift from fossil-based to bio-based production, reducing environmental impact and boosting industrial resilience. These innovations pave the way for new value chains and inclusive economic opportunities, particularly in underdeveloped regions.
Overall, the project has validated its scientific and technological approaches while laying a strong foundation for long-term socio-economic and environmental impact—reinforcing Europe’s leadership in a sustainable, microbiome-driven bioeconomy.