H2020 MASTER Project: Microbiome Applications for Sustainable Food Systems through Technologies and Businesses
- Type Project
- Status Filled
- Execution 2019 -2023
- Assigned Budget 10.950.171,9 €
- Scope Europeo
- Main source of financing Horizon 2020
- Project website Proyecto MASTER
Although microorganisms dominate nearly every ecological niche on our planet, it is only in the last 10 to 15 years that we have begun to better understand the composition and function of microbial communities (microbiomes) thanks to significant advances in high-throughput DNA sequencing (HTS) technologies. These approaches have enabled comprehensive microbiome analysis for the first time. Following initial curiosity-driven microbiome research using HTS technologies, the field has evolved to leverage the insights gained, leading to the development of a new multi-billion-dollar industry focused on microbiome characterization and modulation.
The vast majority of this investment has been directed toward the clinical field. Conversely, much less is known about microbiomes in complex food chains, making it difficult to leverage microbial data from the food chain to develop more sustainable food systems and innovative products and applications. This is despite the clear importance of microbes throughout the food chain. MASTER will take a holistic approach to developing specific microbial products, foods, services, or processes with high commercial potential. These products will benefit society by improving food quantity, quality, and safety across multiple food chains, including seafood, plant-based, soil-based, rumen-based, meat-based, brewing, plant-based waste, and fermented foods.
This will be achieved by mining microbial data related to the food chain, developing big data management tools to identify interrelationships between microbiomes along food chains, and generating applications that promote sustainability and circularity, and contribute to waste management and climate change mitigation. We will leverage microbial knowledge to significantly improve the health and resilience of fish, plants, soil, animals, and humans, enhance professional skills and competencies, and support the creation of new jobs in the food sector and the bioeconomy.
Mastering the Plant Microbiome: We developed microbiome-based solutions to improve production, optimize quality, and control diseases in forage crops. Trials with plant growth-promoting strains, plant biocontrol strains, and developed formulations evaluated the compatibility and efficacy of these microorganisms. A pellet formulation for mycorrhizal biofertilizer was developed and introduced to the market. Progress was made in the development of a microbiome-based diagnostic tool for pathogen detection and prediction of colonization efficiency. Mastering the Marine Microbiome: Novel microbiome-based solutions led to increased beneficial effects of sustainable aquaculture feeds. The effect of probiotic strains on fish growth was determined.
In addition, fillet quality and sensory values of Atlantic salmon fed with and without probiotics were evaluated. Promising results were also obtained that contribute to a rapid protocol for pathogen detection in aquaculture systems. Mastering the rumen microbiome: By manipulating the rumen microbiome, MASTER improved ruminant production, while reducing methane emissions and providing healthy meat and dairy products. Large numbers of animals were studied to investigate the impact of rearing, various feed additives, and microbiome modulators on feed efficiency and methane emissions, linking the rumen microbiome to phenotypes. This highlighted several approaches that merit larger-scale application, individually or in combination.
The benefits of modulating the rumen microbiome early in life for health and well-being were also determined, while mathematical models of rumen microbial activity were developed to predict and design additional methane control strategies. MASTERING Food Microbiomes and Human Gut Health: We provide the food industry with updated microbiome mapping procedures to investigate microbial contaminants along food processing lines, which can be applied to improve food quality and safety, reduce holding periods, and reduce food waste. This initiative generated a comprehensive new database that allows DNA sequencing-based approaches to identify microorganisms in the food chain with much greater accuracy. In other work, new food and feed ingredients were developed from food waste, while, in parallel, new biopreservation strategies for seafood and meat were developed.
Microbiome and diet data were also analyzed, exploring the relationship between diet and the gut microbiome and further highlighting the importance of fermented foods as a source of potentially probiotic bacteria. MASTER Standards: We created a unified approach for the analysis of microorganisms in the food chain and standardized validated methods for microbiome processing of samples from different environments and for different types of DNA sequencing. A bioinformatics workflow for profiling metagenomic data from the food chain was developed and implemented. Two databases were created: CuratedFoodMetagenomicDatabase (containing all publicly available food/food production metagenomes, including MASTER data) and foodGenVir (at the level of individual microbial strains or genes associated with traits of interest). The protocols and databases will soon be available on an open web portal after the project's completion (which will be expanded through the DOMINO project) and have the potential to revolutionize food microbiology testing in the future.
Microorganisms exist in every ecological niche: from the surfaces we touch to the foods we eat, and even within us, many of them essential to our health. Previously, scientists used agar plates and microscopes to study these microorganisms, but now we employ DNA sequencing technologies to uncover the composition and potential function of microbial communities.
Scientists across Europe, within the framework of the H2020 MASTER Innovation Action, used these technologies to map microbiomes in diverse food chains, obtaining data for the development of safer, higher-quality, healthier, and more sustainable food systems. Our researchers have extracted this microbiome data, developed big data management tools, identified relationships between microbiomes in food chains, and generated applications that promote sustainability and contribute to waste management and climate change mitigation. MASTER has led to innovative products and applications, such as microbiome-friendly products, food and feed, services, and processes.
Although microorganisms dominate almost every ecological niche on our planet, it has only been in the last 10 to 15 years that we have begun to gain insights into the composition and function of microbial communities (microbiomes) as a result of significant advances in high-throughput DNA sequencing (HTS) technologies. These approaches have enabled comprehensive microbiome analysis for the first time. Following initial curiosity-driven microbiome investigations using HTS technologies, the field has evolved to leverage the insights provided, leading to the development of a new multi-billion-dollar industry focused on microbiome characterization and modulation.
The vast majority of this investment has been in the clinical space. In contrast, much less is known about microbiomes in complex food chains, making it difficult to leverage food chain microbiome data for the development of more sustainable food systems and innovative products and applications. This is despite the evident importance of microbes along the food chain. MASTER will take a comprehensive approach to developing microbiome-specific products, foods/feeds, services, or processes with high commercial potential, which will benefit society by improving food quantity, quality, and safety, across multiple food chains, including seafood, plant-based, soil-based, rumen-based, meat-based, brewing-based, plant-based waste, and fermented foods.
This will be achieved by mining microbiome data related to the food chain, developing big data management tools to identify interrelationships between microbiomes along food chains, and generating applications that promote sustainability, circularity, and contribute to waste management and climate change mitigation. We will leverage microbiome knowledge to significantly improve the health and resilience of fish, plants, soil, animals, and humans, enhance professional skills and competencies, and support the creation of new jobs in the food sector and the bioeconomy.
Microorganisms thrive everywhere, including within us. Pioneering microorganism-based solutions pave the way for sustainable food and feed that promote health, waste reduction, and optimized agriculture. The collection of microorganisms, such as bacteria, fungi, and viruses, known as the microbiome, influences our well-being, influencing everything from digestion to immune response. Microbiomes also exist in all agri-food systems.
Understanding these microorganisms and their complex interactions with each other and their environments is critical to ensuring safer and more sustainable food production. Consistent Procedures for Microbiome Mapping The EU-funded MASTER project focused on deciphering the intricate relationships between microbiomes in interconnected food systems, including marine, plant, soil, rumen, and feed. “Using microbiome-based DNA sequencing technologies, the primary objective was to design systems that would improve the quality, sustainability, and health-promoting capacity of agri-food chains, food, and feed generated,” explains project coordinator Paul Cotter. To achieve this, ensure consistent microbiome analysis, and maintain comparability throughout the food chain, the consortium standardized procedures for sample collection, preservation, and storage. The development of standard operating procedures at all stages of the analysis process minimized potential errors, avoiding bias and misinterpretation of data.
New Technology More specifically, MASTER developed a new protocol and associated DNA extraction kit to facilitate efficient sampling for DNA-based microbiome analysis, even in cases where this proves difficult due to the low presence of microorganisms. Notably, the application of this protocol to thousands of samples from different food processing environments led to the creation of the CuratedFoodMetagenomic database, an invaluable resource that the industry can use to accurately detect microorganisms present in food. These tools can be used in combination with a rapid, portable DNA sequencing tool to detect problematic microorganisms. Improving Food and Feed Production Recognizing the critical role of plant microbiomes in strengthening plant defense mechanisms against pathogens and promoting plant growth, scientists developed microbial strains to combat pathogenic fungi in crops such as corn and biofertilizers to improve grass quality.
In aquaculture, microbiome-based solutions, including probiotic strains and biopreservatives, showed promising results in improving fish growth and fillet quality. MASTER also delved into the microbiome of ruminants such as cows, sheep, and goats. This microbiome is vitally important because, depending on its composition, it can affect the ability to extract protein and other nutrients from animal feed, and it also contributes to greenhouse gas emissions (primarily methane). "Modulating the ruminant microbiome can reduce environmental impact and also lead to sustainable, higher-quality meat and dairy products," Cotter says.
Addressing food waste and beyond Global food waste, which accounts for nearly a third of total food production, was addressed through food processing technology to convert waste into beneficial ingredients. Researchers also studied fermentation as a natural preservation method. “Fermented foods, rich in beneficial bacteria, improve food quality, safety, and digestibility, and offer health benefits,” explains Cotter. A comprehensive study of various fermented foods opens the door to new foods optimized with respect to these attributes. Cotter highlights: “More than 20 innovations have emerged from MASTER, each identified for its immense potential.” Looking ahead, the MASTER consortium will continue research in new EU projects, such as DOMINO and HoloRuminant, ensuring sustained and continued progress in these critical areas.
New formulations for the application of arbuscular mycorrhizal fungi and biocontrol bacteria were developed and tested, with several positive results. The potential of ONT technology for soil-based pathogen detection was also revealed, and new bioinformatics tools were established. Considerable progress was made in optimizing sustainable aquaculture feeds. Progress was made in the rapid detection of fish pathogens in aquaculture systems.
Potential socioeconomic and societal implications include a reduced reliance on fishmeal in aquaculture and more efficient feed utilization. Studies with ruminants have illustrated the potential for raising animals with lower methane emissions, establishing that numerous dietary interventions further reduced methane emissions, increased productivity, and/or ensured nutritious products. The use of phenolic compounds to redirect hydrogen and reduce methane emissions, while providing more energy to the animal, holds great promise. Likewise, the inclusion of microalgae in lamb diets showed health benefits (higher omega-3 content) while reducing methane emissions. Advances in modeling will lead to innovative nutritional strategies for ruminants that seek to mitigate methane and maximize animal health and productivity. MASTER has generated validated procedures for mapping microbiomes in the food industry, promoting process optimization, waste reduction, and improved feed quality and safety.
A map of the interconnections between food products, nutrients, microorganisms, and the human gut microbiome has been established, which will help provide dietary recommendations to benefit human health. MASTER has made significant progress in providing strategies for the biopreservation of seafood and meat. Procedures have also been developed for the valorization of brewery waste streams and fruits to produce foods and ingredients. The positive effect of valorized ingredients on the human gut microbiota has been validated in in vitro colon studies. The development of harmonized protocols, a simulated community, and automated analytical processes within MASTER, specifically dedicated to food-related ecosystems, will enhance the standardization and potential of sequencing technologies for the food chain.
The newly generated MASTER databases provide food-associated microbiome profiles with complementary data, and strains or genes associated with virulence, pathogenicity, spoilage potential, and antimicrobial resistance, which will be essential for the long-term application of sequencing technologies in food analysis. These are novel databases and will be freely available. These results will have important implications, improving the understanding of microbiomes associated with food chains and addressing key societal challenges, including food and nutrition security, health and well-being, food waste management, and climate change adaptation and mitigation.
- TEAGASC - AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY
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