Integrating a holistic perspective in microbiome research for resilient, competitive and sustainable food systems

Microbiomes hold immense potential for food systems applications, but microbiomes are often studied in siloes or one ecosystem at a time. Unlocking the functional diversity of food microbiomes to help develop innovative applications requires a systems approach[[ Meisner, A., Wepner, B., Kostic, T., van Overbeek, L.S. Bunthof, C. J., de Souza, R. S. C., Olivares, M., Sanz, Y., Lange, L., Fischer, D., Sessitsch, A., Smidt, H. (2022). Calling for a systems approach in microbiome research and innovation. Current Opinion in Biotechnology, 73, 171–178. https://doi. org/10.1016/j.copbio.2021.08.003]]. The topic is relevant to the EU policies related to the Commission communication on: Building the future with nature: Boosting Biotechnology and Biomanufacturing in the EU[[https://research-and-innovation.ec.europa.eu/document/download/47554adc-dffc-411b-8cd6-b52417514cb3_en]], the Life Science Strategy, the EU Biodiversity Strategy for 2030, the Zero Pollution Action Plan, the EU strategy on research and technology infrastructure, the R&I Food 2030 Framework and the policies related to the digital transition (e.g. AI Act, etc) and contributes to climate action and biodiversity goals.

Proposals should address all the following activities:

• establish a holistic system approach to study the microbiome, and its interaction with its host and/or environment, its function and contribution to ecosystem(s) functions, connecting inter and trans-disciplinary fields of science (e.g. microbiology, ecology, AI and bioinformatics, biotechnology, synthetic/molecular biology, agronomy, plant sciences, etc.);
• investigate existing and new supporting technologies such as multi-omics technologies, high-throughput sampling/phenotyping systems, predictive models, AI, federated learning, cultivation methods and/or in-vitro validated models (e.g. organoids, organ-on-a-chip, genetic and metabolic engineering) for application in integrated microbiome studies;
• establish further synergies between existing infrastructures (for instance, ELIXIR, MIRRI, BBMRI-ERIC, EOSC, etc.) to enhance their capacity to integrate and valorise integrated microbiome data (integrating samples and associated (meta)-data from diverse sources) as well as considering the integration of other environmental, agricultural, nutritional or climate datasets;
• provide references strains and/or samples (e.g. for food safety or holobiont selection), standard protocols, operating procedures and quality control measures through the existing biobanks and data-repositories to support and facilitate further microbiome studies.

Proposals must follow a multi-actor approach, engaging researchers, businesses (including SMEs and startups), public authorities and policy makers, research infrastructures and civil society to co-develop solutions.