Research & Innovation - Participant Portal


TOPIC : Microbiome applications for sustainable food systems

Topic identifier: LC-SFS-03-2018
Publication date: 27 October 2017
Focus area: Building a low-carbon, climate resilient future (LC)

Types of action: IA Innovation action
Opening date:
31 October 2017
Deadline: 13 February 2018 17:00:00

Time Zone : (Brussels time)
  Horizon 2020 H2020 website
Pillar: Societal Challenges
Work Programme Year: H2020-2018-2020
Topic Updates
  • 08 June 2018 16:18

    Letters informing on the results of the evaluation have been sent to applicants.

    Under the tab 'Topic conditions and documents' the following document is available in the last section "Additional documents": H2020-SFS-2018-1-single stage flash call info

  • 05 March 2018 11:50

    An overview of the number of proposals submitted is now available under the ‘Topic conditions & documents’ section on the topic page.

Topic Description
Specific Challenge:

The EU food system is an important part of the economy and society in Europe. Given the current context of societal, environmental and economic changes, there is need for constant improvement in terms of productivity, quality, safety, market orientation, adaptability, and international competitiveness. Knowledge of the potential of microbial systems, or microbiomes, throughout the food chains, is a promising means to this end. Microbiomes are known to regulate the productivity and health of major food sources such as plants and animals of both terrestrial and aquatic origin, therefore playing a major role in food and nutrition security. They also play a major role in food and feed processing and metabolism in different organisms throughout the evolutionary scale, ultimately influencing human health. A better understanding of the microbiomes associated with the food system[1] would help address a number of key societal challenges including food and nutrition security, health and wellbeing, food waste management, climate change adaptation and mitigation.


Proposals[2] shall focus on concrete microbiome applications which are of benefit to the food system. Building on knowledge already accrued from the isolation and characterization of microbiota associated to food production systems (plants, soils, animals, marine), proposals should look into ways to improve the quantity, quality and safety of the food we produce and consume in Europe. Microbiome applications in the treatment of food waste and alternative uses which promote sustainability and circularity are also included in the scope. Proposals are expected to develop holistic approaches across all stages of the food system from fork to farm including aquatic (marine and fresh water) resources. Activities shall also aim at increasing knowledge and applications derived from the marine microbiome for the development of new products, services or processes for food and health, while contributing to climate change mitigation. The inter-relations among microbiomes from different components across food chains - from soil to plants, animals, the marine and the human gut - and their impact on food and nutrition security and health shall also be considered. International co-operation, transdisciplinary research, and integration of SSH and RRI including gender aspects to ensure long-lasting implementation of the results are encouraged. Activities shall build on existing data and knowledge on the microbiomes associated to food production and processing systems, including results of EU funded projects in FP7 and Horizon 2020. Activities shall optimise the use of pre-existing databases and research infrastructures (including the distributed and virtual ones) and the opportunities granted by big data management tools, thus ensuring interoperability, standard methods and enhanced networking. The interdisciplinary and cross-sectorial nature of the project should also apply to training activities improving the professional skills and competencies and supporting the creation of new jobs in the food sector and the bioeconomy.

The Commission considers that proposals requesting a contribution from the EU of the order of EUR 10 million would allow this specific challenge to be addressed appropriately. Nonetheless, this does not preclude submission and selection of proposals requesting other amounts.

Expected Impact:

In the framework of SDG no 2, 3, 9, 12, 13 and 15, the EU's Bioeconomy Strategy 2012, and the FOOD 2030 SWD[3], and the Blue Economy communication[4], proposals should explain how activities included are expected to:

  • Raise awareness of the potential behind microbiomes from terrestrial and aquatic environments in transforming and future-proofing our food system;
  • Bring to market new and cost-effective commercial applications to assist different stages and processes throughout the food chains, by 2025;
  • Improve overall knowledge of microbiomes from land and seas towards the market needs in areas where applicability and readiness is not visible;
  • Improve overall sustainability, including climate change mitigation, and innovation capacity of the food system through the use of microbiome applications and knowledge;
  • Move available solutions from TRL 5/6 to TRL 7.
Cross-cutting Priorities:

Blue Growth
Socio-economic science and humanities
International cooperation

[1] A food system is defined as a system that embraces all the elements (environment, people, inputs, processes, infrastructure, institutions, markets and trade) and activities that relate to the production, processing, distribution and marketing, preparation and consumption of food and the outputs of these activities, including socio-economic and environmental outcomes. A sustainable food system is a food system that delivers food and nutrition security for all in such a way that the economic, social and environmental bases to generate food security and nutrition for future generations are not compromised.

[2]Complementary topics presented in the Work Programme are: SC1-BHC-03-2018 Exploiting research results and potential of the human microbiome for personalised prediction and prevention of disease, SFS-01-A-2018: Small organisms, big effects for plants - Belowground biodiversity interaction with plants, SFS-02-2020 Healthy livestock gut ecosystem for sustainable production



Topic conditions and documents

1. Eligible countries: described in Annex A of the Work Programme.
A number of non-EU/non-Associated Countries that are not automatically eligible for funding have made specific provisions for making funding available for their participants in Horizon 2020 projects. See the information in the Online Manual.


2. Eligibility and admissibility conditions: described in Annex B and Annex C of the Work Programme. SME instrument: described in the Work Programme part "European Innovation Council (EIC)".


Proposal page limits and layout: please refer to Part B of the proposal template in the submission system below.


3. Evaluation:

4. Indicative time for evaluation and grant agreements:

Information on the outcome of evaluation (single-stage call): maximum 5 months from the deadline for submission.
Signature of grant agreements: maximum 8 months from the deadline for submission.

Information on the outcome of evaluation (two-stage call):
For stage 1: maximum 3 months from the deadline for submission.
For stage 2: maximum 5 months from the deadline for submission.
Signature of grant agreements: maximum 8 months from the deadline for submission.

5. Proposal templates, evaluation forms and model grant agreements (MGA):

Innovation Action:

Specific provisions and funding rates
Standard proposal template
Standard evaluation form
General MGA - Multi-Beneficiary
Annotated Grant Agreement

6. Additional provisions:

Horizon 2020 budget flexibility
Classified information
Technology readiness levels (TRL) – where a topic description refers to TRL, these definitions apply

Members of consortium are required to conclude a consortium agreement, in principle prior to the signature of the grant agreement.

8. Additional documents:

1. Introduction WP 2018-20
9. Food security, sustainable agriculture and forestry, marine and maritime and inland water research and the bioeconomy WP 2018-20
18. Dissemination, Exploitation and Evaluation WP 2018-20

General annexes to the Work Programme 2018-2020

Legal basis: Horizon 2020 Regulation of Establishment
Legal basis: Horizon 2020 Rules for Participation
Legal basis: Horizon 2020 Specific Programme

Legal basis: EIT Strategic Innovation Agenda

7. Open access must be granted to all scientific publications resulting from Horizon 2020 actions.

Where relevant, proposals should also provide information on how the participants will manage the research data generated and/or collected during the project, such as details on what types of data the project will generate, whether and how this data will be exploited or made accessible for verification and re-use, and how it will be curated and preserved.

Open access to research data
The Open Research Data Pilot has been extended to cover all Horizon 2020 topics for which the submission is opened on 26 July 2016 or later. Projects funded under this topic will therefore by default provide open access to the research data they generate, except if they decide to opt-out under the conditions described in Annex L of the Work Programme. Projects can opt-out at any stage, that is both before and after the grant signature.

Note that the evaluation phase proposals will not be evaluated more favourably because they plan to open or share their data, and will not be penalised for opting out.

Open research data sharing applies to the data needed to validate the results presented in scientific publications. Additionally, projects can choose to make other data available open access and need to describe their approach in a Data Management Plan.

Projects need to create a Data Management Plan (DMP), except if they opt-out of making their research data open access. A first version of the DMP must be provided as an early deliverable within six months of the project and should be updated during the project as appropriate. The Commission already provides guidance documents, including a template for DMPs. See the Online Manual.

Eligibility of costs: costs related to data management and data sharing are eligible for reimbursement during the project duration.

The legal requirements for projects participating in this pilot are in the article 29.3 of the Model Grant Agreement.


Additional documents

  • Flash call info - SFS single stage_en

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