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Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

Periodic Reporting for period 1 - MASTER (Microbiome Applications for Sustainable food systems through Technologies and EnteRprise)

Reporting period: 2019-01-02 to 2020-07-01

Microorganisms exist in most 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. We can discover the make-up and function of microbial communities (microbiomes) using DNA sequencing technologies. Scientists across Europe within the H2020 Innovation Action MASTER (Microbiome Applications for Sustainable food systems through Technologies and EnteRprise) are using these technologies to map microbiomes across a range of food chains, acquiring data for the development of safer and more sustainable food systems. MASTER researchers are mining this microbiome data, developing big data management tools, identifying relationships between microbiomes across food chains and generating applications that promote sustainability and contribute to waste management and climate change mitigation. MASTER is yielding innovative products and applications such as microbiome products (strains, strain mixtures and kits), foods and feeds, services and processes. Research spans multiple food chains (marine, plant, soil, rumen, meat, brewing, fruit and vegetable waste and fermented foods) and will benefit society by improving food quantity, quality and safety.
Work has commenced across all work packages in the first 18 months of the project.

MASTERing plant microbiomes: MASTER will provide microbiome-based solutions to improve production, enhance quality and control disease in typical fodder crops. Trials with plant growth-promoting and bio-control strains assessed their compatibility and effectiveness, and larger (field) trials were planned. The development of microbiome-based diagnostic tools enabling the detection of plant pathogens began, following the optimization of protocols and the selection of plant pathogens.

MASTERing marine microbiomes: Microbiome-based solutions being developed include increasing the beneficial effects of sustainable aquafeeds by influencing the fish gut microbiome. The effect of a range of probiotic strains on growth performance of two fish species was determined. Exciting results contributing to a rapid protocol for pathogen detection in aquaculture systems using state-of-the-art sequencing were also generated.

MASTERing rumen microbiomes: Through the manipulation of the rumen microbiome MASTER will improve ruminant production while reducing methane (a greenhouse gas) emissions and providing healthy meat and milk products for the consumer. Thus far a large number of beef and dairy cattle and lambs were studied to investigate feed efficiency (success with which food is converted to muscle or milk) and methane emission. We are now investigating the use of rapid microbiome testing to determine feed efficiency/methane production. The methane inhibitory capacity of microalgae and a number of feed supplements produced from agro-industrial by-products was monitored. These studies are being combined with the development of advanced mathematical models of microbial activity in the rumen to predict and design further methane control strategies.

MASTERing food microbiomes and human gut health: From this research we will provide the food industry with up-to-date microbiome mapping procedures to investigate microbial contaminants along food processing lines, with the aim of enhancing food quality and safety and reducing withholding periods and food waste. Protocols for sample collection from food industries have been developed. Over 120 food industries across Europe have agreed to take part in the campaign; with sampling completed at 74 industries. Work also focused on the characterization of vegetable and brewery waste materials with a view to developing novel food and feed ingredients. Brewers spent grain was fermented and developed into ingredients for bread and pasta products with increased fibre content. In other work, microbiome and dietary data were analysed to explore the relationships between diet and the gut microbiome, and the importance of fermented foods as a source of potentially probiotic lactic acid bacteria in the human gut metagenome was established.

MASTERing standards: Within MASTER we are creating a unified approach to the analysis of food chain microorganisms and have standardized validated methods for microbiome processing of samples from different environments and for different types of DNA sequencing. The database CuratedFoodMetagenomicData was created, which includes all publicly available microbiome samples derived from studies on metagenomes of food or food-production. To produce a long-term resource beyond the end of the project, the protocols and databases will be available in an open web portal.
In this reporting period, new insights into interactions between bacterial (biofertilizing and biocontrol) strains and arbuscular mycorrhiza fungi (AMF) with biofertilising abilities were observed, paving the way for future combined microbiome products for increased plant growth and health. Progress had also been made towards optimizing sustainable aquafeeds for the aquaculture industry, including the use of tailored prebiotics and probiotics. Progress was also made towards the rapid detection of fish pathogens in open and closed aquaculture systems, having implications for aquaculture farms as well as for pathogen control in natural habitats. Potential socio-economic and wider societal implications include a reduction of the dependence on the use of fish meal in the aquaculture industry and more efficient feed utilization, which will benefit natural resources management.

In ruminant research, supplementation with microalgae is expected to reduce methane emissions, increase animal efficiency performance and improve meat quality. Our parallel modeling developments will contribute to the design of further cutting edge ruminant nutritional strategies for methane mitigation that will maximize health and animal productivity.

MASTER is generating validated procedures to map microbiomes in the food industry, promoting process optimization, waste reduction and improving food quality and safety. A map of the interconnections between food products, nutrients, microorganisms and the human gut microbiome is being established and will provide dietary recommendations to benefit human health through gut microbiome modulation. MASTER researchers are also providing a detailed characterization of brewery and vegetable waste streams to understand the suitability and functionality of such by-products for the development of innovative, functional and health-promoting ingredients.

Development of harmonized protocols and automated analytical pipelines within MASTER especially dedicated to food-related ecosystems will improve the potential of sequencing technologies for the food chain. Newly generated MASTER databases provide profiles of food-associated microbiomes, with accompanying data, that will be essential for the longer term application of sequencing technologies for food testing. These are novel databases and will be freely available to be used by the scientific community and industries.

All of 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.

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