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  6. Willett W.,   et al., Lancet, 393, 447-492 (2019).
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  8. Caron P., et al., Agron. Sustain. Dev., 38, 41 (2018).
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  11. Wu Y., et al., Annu. Rev. Food Sci. Technol., 10, 389-408 (2019).
  12. Marco M.L., et al., Curr. Opin. Biotechnol., 44, 94-102 (2017).
  13. O’Sullivan L., et al., Annu. Rev. Food Sci. Technol., 10, 151-172 (2019).
  14. ALLEA Working Group ‘Truth, Trust & Expertise’, ALLEA Discussion Papers,  (2019).
  15. De Filippis F., et al., Annu. Rev. Food Sci. Technol., 9, 589-608 (2018).
  16. International Bioeconomy Forum: https://ec.europa.eu/research/bioeconomy/index.cfm?pg=policy&lib=ibf (last checked on Aug, 12th 2019).
  17. MicrobiomeSupport project: www.microbiomesupport.eu (last checked on Aug, 12th 2019).

The current food system is unable to meet the increasing demand for nutritious, safe and sustainable food (4). Various international and national organisations and governments have recognised the need for a transformation of the food system and have provided suggestions on how to do so at different levels. For instance,

  • The UN Collaborative Framework for Food Systems Transformation emphasises the need for a collaborative approach for policy-making and implementation (5);
  • The European Commission’s FOOD 2030 policy initiative recommends a system-wide approach for transformation (4);
  • The EAT Lancet Commission suggests a largely plant-based diet for all (6);
  • IPES Food recommends a common food policy for the EU (7);
  • Scientists suggest an alignment with the Sustainable Development Goals (8).

The general consensus is to transform the food system in an inclusive, resource-efficient and sustainable manner whilst providing healthy and nutritious foods to all.


    Microbes are everywhere in the food web. In communities they support, for instance, soil health and crop productivity, and can protect from livestock diseases and food poisoning (9, 10). Scientific understanding about the microbiome and the links with human health is rapidly increasing (e.g. 11) and the general public’s interest in capitalising on these effects is growing (e.g. through fermented foods; 12). Furthermore, the microbiome may hold the key to tackling major societal challenges like climate change (9). Altogether, this makes leveraging the potential of micro-organisms timely (3).


      With the rising recognition of the potential of microbes in the food system to meet global challenges, calls for education, policy and other reforms need to take into account the potential of the microbiome. Further, global initiatives with long-term commitment to research, engagement around the research process and outcomes, as well as implementation of innovative solutions are essential to bridge the gap between today’s potential and tomorrow’s microbiome solutions (3).

      The MicrobiomeSupport project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 818116.

        WHAT NOW?

        Understanding the challenges and opportunities in microbiome research and openly communicating and engaging all food system actors in the process (from farmers, to small and big food processors, food distributers and retailers, food consumers and food waste processors) will facilitate a microbiome-based food system transformation. This includes identifying the existing challenges; for instance:

        • Published microbiome research is currently still limited to observatory studies in humans, and information in non-human (e.g. plant, soil and animal) health research is hidden or not easily available, particularly to lay people;
        • The difficulties of bridging the lab-field gap (e.g. how do agricultural practices affect microbial communities in the field?; 10);
        • The unaligned approach to research across different funding bodies on different geo-political levels leading to duplication of resources (3);
        • Legislation for food safety or medical products is often focused on individual micro-organisms only, rather than microbial communities;
        • Non-aligned research methods across and within fields leads to seemingly contradictory findings (3);
        • Lack of understanding and agreement in the research communities on whether to focus on microbial species within a community or the functions these microbes provide or both;
        • Potential risks, e.g. new bacterial resistances due to the use of bacteriophages for food safety applications (13).

        Yet opportunities are abounding:

        • There is an increasing awareness of and interest in the microbiome in the media and the general public, i.e. there is potential for early communication with affected food system actors (everyone who produces, processes, eats and wastes food) on the potential risks and benefits as well as current limitations in microbial research to increase understanding of why the microbiome is important and how it is relevant to the wider community (14);
        • Technological breakthroughs are facilitating more discoveries than ever (10,13,15);
        • There is political momentum to explore joint efforts on microbiome applications internationally with the European Union and Canada heading the International Bioeconomy Forum Working Group ‘Food Systems Microbiome’ (with support from Argentina, China, India, New Zealand, South Africa, the US, as well as Australia and South Korea as observers; 16).

        The EU-funded project MicrobiomeSupport (Horizon 2020 grant agreement No 818116; 17;), coordinated by Dr Angela Sessitsch at the Austrian Institute for Technology, is taking advantage of these opportunities and aims to provide solutions to some of the challenges microbiome research currently faces. The project aims to:

        • Set quality standards for microbiome research globally and across disciplines;
        • Support the International Bioeconomy Form Working Group ‘Food System Microbiomes’ and the implementation of the FOOD 2030 policy initiative;
        • Engage all food system actors to communicate on the benefits and challenges of microbiome research and to overcome short-term thinking;

        Align research funding worldwide to avoid duplication of efforts.



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