Engineering Microbial Consortia

Microbial consortia perform industrial work today at large scale and low cost, including biogas production, composting, wastewater treatment, and the fermentations behind many foods. Stable natural consortia are robust to changing environments, feed, and contaminants and can grow on cheap, variable inputs. However, these natural communities are difficult to steer towards new intended products. Precision fermentation can use a single engineered organism in a reliable production process to produce high value goods. However, this approach requires costly infrastructure: sterile reactors, purified feedstocks, and tight environmental control.

Between these two modes of industrial biotechnology, promising new capabilities are being demonstrated in the lab. Synthetic consortia, using division of labour and specialisation, can build molecules of higher complexity efficiently across multiple strains or organisms grown together in co-culture. Natural consortia, using varied models for predictive control, can be steered towards valuable products such as fatty acids and commodity chemical precursors in open, non-sterile processes.

This Challenge would aim to bring new microbial consortia-based approaches to manufacturing into routine commercial use. Our ambition is to find breakthrough innovations in the gap between current precision fermentation and current industrial environmental biotechnology. Our hypothesis is that with new data, new tools, and new AI models, predictive control of natural and synthetic consortia can be directed to radically new functions and valuable products.

We are interested in the production of chemicals, materials, fuels, and other molecules by microbial communities, where this could advance biomanufacturing, the circular economy, and sustainable manufacturing. We would like to hear from teams working on industrial and bio-based production, and we welcome views on how far this opportunity extends into adjacent areas such as agricultural production.

We are also interested in groups whose tools and methods for measuring, modelling, or steering microbial communities could transfer to manufacturing, including those working in health and the microbiome. At this stage we seek to learn broadly across all of these fields, though this potential Challenge would focus on manufacturing, not therapeutics or diagnostics. Approaches of every kind are of interest for this Request, from synthetic consortia with an engineered division of labour to the enrichment, evolution, and control of natural and open communities.

• Where are the strongest opportunities for synthetic and natural consortia-based production?
• Which under-developed waste and side-streams could consortia use in a bio-based circular economy?
• Which new products and markets could this approach reach?
• What is the current state of the art? Which capabilities have been demonstrated convincingly, and where is the distance between a laboratory result and commercial use greatest?
• What are the main barriers to operating engineered or steered communities reliably at industrial scale? In open, non-sterile conditions? With varied feedstocks?
• What tools, measurements, or datasets are missing across the field, and what would it take to create them? Where could data and AI methods make community behaviour predictable, and what would be needed first?
• What opportunities exist for consortia-based production of materials, structural bio-products, or other non-molecular goods? This Challenge will focus on manufactured products, and we expect environmental remediation, ecosystem services, and environmental release of consortia to be out of scope.
• Which groups, companies, and individuals are doing the most relevant work, in Europe and beyond?
• How could public funding be most useful in this area, and what should a programme like this avoid?
• What metrics are most important to include in the evaluation of proposed projects for this Challenge, both at the beginning of the project and as final project milestones?

Past SPRIND Challenges have been open to teams headquartered in the European Union, the European Free Trade Association, the United Kingdom, or Israel, with individual team members or collaborators permitted to be based elsewhere. Teams of every kind have taken part, from universities and research institutions to established companies and startups; what they share is an ambition to bring a breakthrough innovation to market, whether through an existing company or one founded early during the Challenge.

Recent Challenges have run in three year-long stages, with teams re-selected competitively against the Challenge's goals for each stage; up to €1.5 million for the first stage, €2.0 million for the second, and €2.5 million for the third.  This potential Challenge is expected to follow a similar structure, though the exact details will differ.

We would welcome responses you may have to any of the questions we pose, and your suggestions for whom else we should speak with as we explore this opportunity. Submissions to this RFI will be reviewed on a rolling basis until 03 August. If you would like to share commercially sensitive information, contact us in advance of submitting confidential materials. Please feel free to circulate the RFI link to your colleagues.

Respectfully,

Joseph Meyerowitz, Challenge Manager
joe.meyerowitz@sprind.org

Hannah Klein, Challenge Officer hannah.klein@sprind.org

Last Updated: 21 July 2026