Periodic Reporting for period 3 - MASTER (Microbiome Applications for Sustainable food systems through Technologies and EnteRprise)
Berichtszeitraum: 2022-01-02 bis 2023-07-01
Microorganisms exist across all ecological niches; from the surfaces we touch, to the foods we eat and also inside of us, with many microorganisms being integral to our health. Scientists previously used agar plates and microscopes to study these microorganisms but now we use DNA sequencing technologies to discover the make-up and potential function of microbial communities. Scientists across Europe in the H2020 Innovation Action MASTER used these technologies to map microbiomes across a range of food chains, acquiring data for the development of safer, higher quality, healthier and more sustainable food systems. Our researchers have mined this microbiome data, developed big data management tools, identified relationships between microbiomes across food chains and generated applications that promote sustainability and contribute to waste management and climate change mitigation. MASTER has yielded innovative products and applications, such as microbiome products, foods and feeds, services and processes.
MASTERing plant microbiomes: We developed microbiome-based solutions to improve production, enhance quality and control disease in fodder crops. Trials with plant growth-promoting, plant biocontrol strains and developed formulations assessed the compatibility and effectiveness of these microorganisms. A pellet formulation for mycorrhiza-based biofertiliser was developed and introduced to the market. Development of a microbiome-based diagnostic tool for pathogen detection/prediction of colonisation efficiency was advanced.
MASTERing marine microbiomes: New microbiome-based solutions led to an increase in the beneficial effects of sustainable aquafeeds. The effect of probiotic strains on fish growth performance was determined. Furthermore, the fillet quality and sensory values of Atlantic salmon, fed with and without probiotics, were evaluated. Exciting results contributing to a rapid protocol for pathogen detection in aquaculture systems were also generated.
MASTERing rumen microbiomes: By rumen microbiome manipulation, MASTER improved ruminant production while reducing methane emissions and providing healthy meat and milk products. A large number of animals were studied, investigating the impact of breeding, a variety of feed additives and microbiome modulators on feed efficiency and methane emissions, linking rumen microbiome with phenotypes. This highlighted a number of approaches that merit application, individually or in combination, on a wider scale. The benefit of early life rumen microbiome modulation in terms of health and welfare was also determined, whilst developing mathematical models of microbial activity in the rumen, to predict and design further methane control strategies.
MASTERing food microbiomes and human gut health: We provided the food industry with up-to-date microbiome mapping procedures to investigate microbial contaminants along food processing lines, which can be applied to enhance food quality and safety and reduce withholding periods and food waste. Through this initiative, a new comprehensive database was generated to allow DNA sequencing based approaches to much more accurately identify microorganisms present in the food chain. In other work, novel food/feed ingredients were developed from food waste materials, while, in parallel, novel seafood and meat biopreservation strategies were developed. Microbiome and dietary data was also analysed, exploring the diet-gut microbiome relationship and further highlighting the importance of fermented foods as a source of potentially probiotic bacteria.
MASTERing standards: We created a unified approach to the analysis of food chain microorganisms, and standardised validated methods for microbiome processing of samples from different environments and for different types of DNA sequencing. A bioinformatics workflow for food-chain metagenomic data profiling was developed and implemented. Two databases were created: CuratedFoodMetagenomicDatabase (contains all publicly available metagenomes of food/food production, including MASTER data) and foodGenVir (at the level of single microbial strains or genes associated with traits of interest). The protocols and databases will soon be available in an open web portal beyond the end of the project (to be further expanded through the DOMINO project), and have the potential to revolutionize food microbiology testing in the future.
MASTERing marine microbiomes: New microbiome-based solutions led to an increase in the beneficial effects of sustainable aquafeeds. The effect of probiotic strains on fish growth performance was determined. Furthermore, the fillet quality and sensory values of Atlantic salmon, fed with and without probiotics, were evaluated. Exciting results contributing to a rapid protocol for pathogen detection in aquaculture systems were also generated.
MASTERing rumen microbiomes: By rumen microbiome manipulation, MASTER improved ruminant production while reducing methane emissions and providing healthy meat and milk products. A large number of animals were studied, investigating the impact of breeding, a variety of feed additives and microbiome modulators on feed efficiency and methane emissions, linking rumen microbiome with phenotypes. This highlighted a number of approaches that merit application, individually or in combination, on a wider scale. The benefit of early life rumen microbiome modulation in terms of health and welfare was also determined, whilst developing mathematical models of microbial activity in the rumen, to predict and design further methane control strategies.
MASTERing food microbiomes and human gut health: We provided the food industry with up-to-date microbiome mapping procedures to investigate microbial contaminants along food processing lines, which can be applied to enhance food quality and safety and reduce withholding periods and food waste. Through this initiative, a new comprehensive database was generated to allow DNA sequencing based approaches to much more accurately identify microorganisms present in the food chain. In other work, novel food/feed ingredients were developed from food waste materials, while, in parallel, novel seafood and meat biopreservation strategies were developed. Microbiome and dietary data was also analysed, exploring the diet-gut microbiome relationship and further highlighting the importance of fermented foods as a source of potentially probiotic bacteria.
MASTERing standards: We created a unified approach to the analysis of food chain microorganisms, and standardised validated methods for microbiome processing of samples from different environments and for different types of DNA sequencing. A bioinformatics workflow for food-chain metagenomic data profiling was developed and implemented. Two databases were created: CuratedFoodMetagenomicDatabase (contains all publicly available metagenomes of food/food production, including MASTER data) and foodGenVir (at the level of single microbial strains or genes associated with traits of interest). The protocols and databases will soon be available in an open web portal beyond the end of the project (to be further expanded through the DOMINO project), and have the potential to revolutionize food microbiology testing in the future.
New formulations for the application of arbuscular mycorrhizal fungi and biocontrol bacteria were developed and tested with several positive outcomes. The potential of ONT technology for pathogen detection in soil was also revealed and new bioinformatic tools established. Considerable progress was made towards optimizing sustainable aquafeeds. Advances were made towards the rapid detection of fish pathogens in aquaculture systems. Potential socio-economic and wider societal implications include a reduction of the dependence on the use of fish meal in aquaculture and more efficient feed utilisation.
Ruminant studies illustrated the potential to breed animals that emit lower methane levels, while establishing that numerous dietary interventions further reduced methane emissions, increased productivity and/or ensured nutritious products. The use of phenolic compounds to re-direct hydrogen and provide reduced methane emissions, while providing more energy to the animal, shows great promise. Likewise, microalgae as part of the diet of lambs showed a benefit to the health-properties of the lamb (higher omega-3 content), whilst also reducing methane emissions. Modelling developments will lead to additional cutting-edge ruminant nutritional strategies for methane mitigation, maximizing health and animal productivity.
MASTER has generated validated procedures to map microbiomes in the food industry, promoting process optimisation, waste reduction and improving food quality/safety. A map of the interconnections between food products, nutrients, microorganisms and the human gut microbiome was established and will help with providing dietary recommendations to benefit human health. MASTER has made significant progress towards the availability of strategies for the biopreservation of seafood and meat. Procedures for the valorisation of brewing and fruit waste streams to produce food/ingredients have also been developed. The positive effect of the valorised ingredients on the human gut microbiota has been validated in in-vitro colon studies.
Our development of harmonised protocols, a mock community and automated analytical pipelines within MASTER, especially dedicated to food-related ecosystems will improve the standardisation and potential of sequencing technologies for the food chain. Newly generated MASTER databases provide profiles of food-associated microbiomes, with accompanying data, and strains or genes associated with virulence, pathogenicity, spoilage potential and antimicrobial resistance that will be essential for the longer-term application of sequencing technologies for food testing. These are novel databases and will be freely available.
These outcomes will have major implications, enhancing understanding of the microbiomes associated with food chains and addressing key societal challenges including food and nutrition security, health and wellbeing, food waste management and climate change adaptation and mitigation.
Ruminant studies illustrated the potential to breed animals that emit lower methane levels, while establishing that numerous dietary interventions further reduced methane emissions, increased productivity and/or ensured nutritious products. The use of phenolic compounds to re-direct hydrogen and provide reduced methane emissions, while providing more energy to the animal, shows great promise. Likewise, microalgae as part of the diet of lambs showed a benefit to the health-properties of the lamb (higher omega-3 content), whilst also reducing methane emissions. Modelling developments will lead to additional cutting-edge ruminant nutritional strategies for methane mitigation, maximizing health and animal productivity.
MASTER has generated validated procedures to map microbiomes in the food industry, promoting process optimisation, waste reduction and improving food quality/safety. A map of the interconnections between food products, nutrients, microorganisms and the human gut microbiome was established and will help with providing dietary recommendations to benefit human health. MASTER has made significant progress towards the availability of strategies for the biopreservation of seafood and meat. Procedures for the valorisation of brewing and fruit waste streams to produce food/ingredients have also been developed. The positive effect of the valorised ingredients on the human gut microbiota has been validated in in-vitro colon studies.
Our development of harmonised protocols, a mock community and automated analytical pipelines within MASTER, especially dedicated to food-related ecosystems will improve the standardisation and potential of sequencing technologies for the food chain. Newly generated MASTER databases provide profiles of food-associated microbiomes, with accompanying data, and strains or genes associated with virulence, pathogenicity, spoilage potential and antimicrobial resistance that will be essential for the longer-term application of sequencing technologies for food testing. These are novel databases and will be freely available.
These outcomes will have major implications, enhancing understanding of the microbiomes associated with food chains and addressing key societal challenges including food and nutrition security, health and wellbeing, food waste management and climate change adaptation and mitigation.