Resources

DOMINO will create several resources about the project and its outcomes.

A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset

Zhang E, Breselge S, Carlino N, Segata N, Claesson MJ, Cotter PD. A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset. iScience. 2025;28:112139. doi:10.1016/j.isci.2025.112139

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Piperni, Elisa et al. Cell, Volume 187, Issue 17, 4554 – 4570.e18

Microbiome Metabolic Modeling as a tool for innovation in fermented foods

The review provides an overview of current research utilizing genome-scale metabolic modeling (GSMM) in fermented food science. An integrated and unified strategy for designing food microbiomes using both bottom-up and top-down GSMM strategies is proposed. Challenges, bottlenecks and perspective of GSMM in fermented food science is discussed.

Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes

The study of microbial metabolic interactions within food microbiomes represents a key scientific approach for improving the quality and health benefits of food. In such studies, methods based on gene expression levels (metatranscriptomic) analysis are promising. However specific tools are required to overcome the challenges posed by food microbiomes, in particular the high variability of microbiomes between samples and the difficulty of automatically inferring the annotation of metabolic functions across taxa. To address this gap, we present the Food Microbiome Metabolic Modules (F3M) tool suite. The F3M suite provides a robust framework for uncovering functional dynamics within food microbiomes. The F3M tool suite is available as open-source.

Edible microbiome and dietary microbiota: bridging two interrelated concepts

The ‘edible microbiome’ concept, introduced in 2015, hypothesised that plant-associated microbiota may, after consumption, significantly impact human health. In parallel, several studies have focused on the potential benefits of ‘live dietary microbe intake’, with a particular focus on foods and supplements that contain high levels of live microorganisms, i.e., fermented foods and probiotic products. Over the past decade, scientific research, including retrospective analysis of dietary surveys and microbiome sequence data, has uncovered new evidence about the roles that food-associated microorganisms play in impacting health after ingestion. In this review, we evaluate the scientific advances that have emerged since the ‘edible microbiome’ concept was proposed, offering insights into how new findings support and expand upon its original premise. We will also propose an evolution of the concept to broaden its scope, incorporating ‘live dietary microbe intake’ more generally, and key research and development opportunities to propel this field forward.

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Fermented foods cards

This page will group all the fermented foods cards prepared by Domino.

Report on Outcomes Living Lab Sessions; Phase 1

Report on outcomes Living Lab sessions up till end of phase 1.

First Update of the Communication, Dissemination and Exploitation plan

The report will provide a summary of activities implemented and outline the plans for the rest of the project at EU level and in each Living Lab country in cooperation with the Living Lab coordinators.

Communication, Dissemination, Exploitation Plan (including project website)

Strategic activities will be planned to maximise the impact of the project. This first CDE plan will include the project website development. It will be updated throughout the project.

First DOMINO Data Management Plan

DOMINO Data Management Plan

Report on current market developments and innovation potential of FF products – secondary market research

Results of a survey that focuses on changes in the production system that are necessary to facilitate FF innovations. Secondary market analysis.

EIP-AGRI Practice Abstracts – Batch 1

This deliverable contains 1 initial practice abstract for the EIP-AGRI portal.

DOMINO Living Lab Manual

Manual with scripts and reporting templates for living lab sessions and results of rapid literature reviews.

Report on Consumer Perceptions of Fermented Foods

Results of a multi-country consumer survey on the perception and acceptance of FF. Results of sensory experiments measuring product acceptance, hedonic liking, and willingness to pay in blind and full information rounds using selected case studies.

Design and Final Version of the FMD

Comprehensive food microbiome database generated at species-level and strain-level with public datasets and with data generated by the Consortium.

First data on food metagenomic and genomic diversity of new microbial strains

Several hundreds of food metagenomic and genomic data of microbial strains, related to the six food case studies of the project, are delivered to our database for consortia design.

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O’Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L; MASTER EU Consortium; Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, Pasolli E. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell. 2024 Aug 16:S0092-8674(24)00833-X. doi: 10.1016/j.cell.2024.07.039. Epub ahead of print. PMID: 39214080.

Which factors drive consumers’ evaluation of fermented foods and drinks? A protocol for a Systematic Map

Geiss and Roosen (2024). Which factors drive consumers’ evaluation of fermented foods and drinks? A protocol for a Systematic Map. https://doi.org/10.17605/OSF.IO/VNKST.

The Systematic Map is supposed to provide insights into consumers’ perspectives on fermented foods. The literature review aims to identify factors that drive the demand, this is, consumers’ evaluation of fermented foods.

Fermented foods – Infographic (English)

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Fermented foods – Infographic (italiano)

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Fermented foods – Infographic (Français)

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Fermented foods – Infographic (eesti keel)

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Fermented foods – Infographic (Español)

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Fermented foods – Infographic (Deutsch)

Microbiome Ambassador Campaign

The #MicrobiomeAmbassador campaign highlights researchers from EU-Funded projects that advocate for the microbiome. Through this campaign, we see the faces behind the research, and get a glimpse into why the microbiome is important for them. Meet our Microbiome Ambassadors from the DOMINO project!

Monitoring the yeasts ecology and volatiles profile throughout the spontaneous fermentation of Taggiasca cv. table olives through culture-dependent and independent methods

Traina, C., Ferrocino, I., Bonciolini, A., Cardenia, V., Lin, X., Rantsiou, K., & Cocolin, L. (2024). Monitoring the yeasts ecology and volatiles profile throughout the spontaneous fermentation of Taggiasca cv. table olives through culture-dependent and independent methods. International Journal of Food Microbiology, 417, 110688. https://doi.org/10.1016/j.ijfoodmicro.2024.110688

Autumn pickled colorful vegetables in jars placed in line

Fermented foods, their microbiome and its potential in boosting human health

Valentino, V., Magliulo, R., Farsi, D., Cotter, P. D., O’Sullivan, O., Ercolini, D., & De Filippis, F. (2024). Fermented foods, their microbiome and its potential in boosting human health. Microbial Biotechnology, 17(2), e14428. https://doi.org/10.1111/1751-7915.14428

Fermented foods – Infographic (English)

Domino – Poster

Domino – Leaflet

Check out the latest DOMINO leaflet to know more about the project!

The power of fermented foods: Levers for healthier and sustainable nutrition

Sproten, R. (2023). The power of fermented foods: Levers for healthier and sustainable nutrition. AgroFOOD Industry Hi Tech, 34(2). Teknoscienze. https://digital.teknoscienze.com/agrofood_industry_hi_tech_34_2_2023/functional_food_-_the_power_of_fermented_foods_levers_for_healthier_and_sustain

Resources

A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Microbiome Metabolic Modeling as a tool for innovation in fermented foods

Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes

Edible microbiome and dietary microbiota: bridging two interrelated concepts

Fermented foods cards

Report on Outcomes Living Lab Sessions; Phase 1

First Update of the Communication, Dissemination and Exploitation plan

Communication, Dissemination, Exploitation Plan (including project website)

First DOMINO Data Management Plan

Report on current market developments and innovation potential of FF products – secondary market research

EIP-AGRI Practice Abstracts – Batch 1

DOMINO Living Lab Manual

Report on Consumer Perceptions of Fermented Foods

Design and Final Version of the FMD

First data on food metagenomic and genomic diversity of new microbial strains

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Which factors drive consumers’ evaluation of fermented foods and drinks? A protocol for a Systematic Map

Fermented foods – Infographic (English)

Fermented foods – Infographic (italiano)

Fermented foods – Infographic (Français)

Fermented foods – Infographic (eesti keel)

Fermented foods – Infographic (Español)

Fermented foods – Infographic (Deutsch)

Microbiome Ambassador Campaign

Monitoring the yeasts ecology and volatiles profile throughout the spontaneous fermentation of Taggiasca cv. table olives through culture-dependent and independent methods

Fermented foods, their microbiome and its potential in boosting human health

Fermented foods – Infographic (English)

Domino – Poster

Domino – Leaflet

The power of fermented foods: Levers for healthier and sustainable nutrition

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