Microbes are everywhere in the food system with different roles:

  • As food itself (e.g. certain algae in marine ecosystems);
  • As food for animals that get consumed as part of the human diet (e.g. fish feeding on plankton in the ocean);
  • As part of foods humans consume, so contributing to human gut microbes which are linked to the human metabolic and immunological health (e.g. on raw produce or in fermented foods);
  • In environments that support soil, crop and livestock health and productivity;
  • In food production (e.g. in fermented produce); and 
  • In food waste decomposition and recycling processes.

In microbial communities and in balance with each other microbes are incredibly important in terms of the productivity and health of the food system through:

  • Keeping potentially harmful micro-organisms in check;
  • Producing metabolic waste products that are beneficial for the host environment (be it in soil, in and on plant tissues, animal or human skin and gut environments).

Communities include a variety of organisms such as bacteria, yeast, viruses and bacteriophages (viruses that kill bacteria). When the individual members of the communities are not in balance with each other and/or when individual micro-organism species have an opportunity to outcompete other community members because of changing environmental conditions, thus shrinking the ecosystem diversity, they can compromise the health of plants, animals, and human beings, as well as lowering soil productivity.


    With being ubiquitous in the food system, microbes have an enormous potential to contribute to solutions that ensure food security in a changing climate. Examples are probiotics, prebiotics, microbial hubs used in agriculture and livestock production for increased yields and higher-quality foods, new natural or pharmaceutical products, process changes in how illness is managed (both in terms of non-communicable and infectious diseases), novel waste and energy management approaches (1-5). Innovative solutions will focus on amplifying the beneficial aspects of microbial communities through optimising environmental conditions as well as combinations of microbes in their respective host environment.

    Research and innovation is slowly expanding to incorporate all parts of the food system and looking at the different parts in an interconnected way (6). For instance, the EU-funded project CIRCLES (7; Horizon 2020 grant agreement No 818290), coordinated by Prof. Marco Candela at the University of Bologna (Italy), investigates microbiome interactions and circulations across seven food chains (spinach, tomatoes, poultry, swine, farmed and wild salmon, and farmed and wild seabream). The aim is to provide scientific knowledge to exploit natural microbiomes for the sustainable production of high-quality food, with the ultimate objective to deliver new and more sustainable food applications.


      Microbiome innovations in the food system are expected to reach the market within the foreseeable future.
      To ensure their successful uptake and encourage adoption of new policies and practices in the production, processing, consumption and wastage of food as well as the management of the associated resources, it is imperative that:

      • Microbiome research funding and methods needs to be aligned across different sectors to increase the validity and comparability of results (2);
      • Risks and benefits of microbial innovations in the food system are clearly communicated in a transparent and timely way to build and embody trust (8-10);
      • Education on the potential of the microbiome and the benefits of microbes (not just their harmful effects) is undertaken (11);
      • Communication with policy, scientific experts and industrial leaders takes place to ensure that the legislatory context can guarantee safe food, health claims are underpinned by solid science and innovative solutions have the potential to come to market within the framework of such regulations (12);
      • Regional, national and international efforts and interests are aligned on both a public and private level (12).

      Microbes in the food system affect everyone, so all people need to be involved in understanding and working with the opportunities and challenges micro-organisms bring to this research and innovation field.

      An inclusive, transparent approach that integrates all players will guarantee an efficient, safe transition to a future-proof food system. CIRCLES will communicate with potential end-users and those affected by microbiome applications by organising City Tours in which citizens can participate in skin sampling activities to learn about their own microbiota. The aim is to communicate openly and responsibly about the risks and benefits, challenges and opportunities in microbiome applications to engage, educate and empower (13).

      The CIRCLES project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 818290.

        WHAT’S NEXT?


        1. de la Calle F. Microb. Biotechnol., 10, 1293-1296 (2017).
        2. Małyska A., et al., Trends Biotechnol., in press (2019).
        3. De Filippis F., et al., Annu. Rev. Food Sci. Technol., 9, 589-608 (2018).
        4. Wu Y., et al., Annu. Rev. Food Sci. Technol., 10, 389-408 (2019).
        5. O’Sullivan L., et al., Annu. Rev. Food Sci. Technol., 10, 151-172 (2019).
        6. Fabbri K., EU Publications, (2017).
        7. CIRCLES: (last checked on Aug, 12th 2019). 
        8. ALLEA Working Group ‘Truth, Trust & Expertise’, ALLEA Discussion Papers,  (2019).
        9. Bortoletti M., Lomax J., UN Environment Publications, (2019).
        10. van der Bles A.M., et al.R. Soc. Open Sci., 6, 181870 (2019).
        11. Timmis K., et al.Environ. Microbiol., 21, 1513–1528 (2019).
        12. Bronzwaer S., et al.EFSA J., 17, 7, (2019).
        13. Shan Y., et al., Nature Medicine,  25, 872-874 (2019).


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