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Sustainable innovation of microbiome applications in food system

Periodic Reporting for period 1 - SIMBA (Sustainable innovation of microbiome applications in food system)

Reporting period: 2018-11-01 to 2020-04-30

The threat of food insecurity is a critical global challenge, compounded by climate change and population growth. Microbiomes are known to regulate the productivity and health of major food sources across land and sea. Therefore, they can positively impact food production, food and nutrition security and ultimately influence human health. However, we lack a deep understanding of the microbiomes associated with our food systems.
SIMBA (Sustainable Innovation of Microbiome Applications in Food System) is a European innovation project, funded through Horizon 2020, which aims to better understanding of microbiome structure and function, related to both marine and terrestrial food chains, and to verify the sustainability of microbial innovations of the food system. SIMBA provides a holistic and innovative approach to the development of microbial solutions to increase food and nutrition security, in particular focusing on the identification of viable land and aquatic microbiomes that can assist in the sustainability of European agro- and aquaculture.
To build on pre-existing knowledge of microbiota associated with marine and land-based food production systems, all publicly available shotgun metagenomic sequence datasets from the Short Read Archive (SRA) international database were collected during the first 18 months of the SIMBA project. Selection criteria were created, including keyword search and literature review, to find SIMBA-related sequence datasets. The common annotated open access database for end users to access collated microbiome data was initiated and is proceeding. The purpose of this database is to support easy access to standardised data for stakeholders working in European food quality, safety and consumption.
To achieve the overall goal to exploit Plant Growth-Promoting Microorganisms (PGPM) for sustainable crop production, an initial literature review to find PGPMs associated with the SIMBA selected crops (maize, wheat, potato and tomato) was carried out to identify efficient microbial formulations and guarantee the development of compatible consortia. Also, a set of bio-active compounds were tested for compatibility in vitro with the single microorganism composing the selected consortia. From this, four main microbial consortia, common to all four crops, were selected and set-up using compatible bacteria with or without the addition of a fungal biocontrol agent and bioactive compounds to support maximum growth. To date, the results are preliminary and ongoing field trials will further inform the efficacy and reproducibility of PGPMs in crop production.
The application of the marine microbiome for food production is still in its infancy. The SIMBA project aims to address the huge potential of the marine ecosystem but also focuses on the inevitable future shortage of freshwater and salinification of arable land in coastal areas. The first 18 months of the project consisted mainly of year-round sampling of unmanipulated algal biomass cultures, seaweed cultures, rhizosphere of natural coastal saltmarshes, rhizosphere of saline agriculture and biofilms. The development of novel healthy fish feed based on combinations of microalgae and fermented plants and seaweeds is almost complete and feeding experiments start in autumn 2020.
The SIMBA project aims to find out and apply microbes that are suitable to convert agricultural residues and raw materials to high quality food, feed or energy. In this first period, data on processing methods and microbes for treating residues and plant-based materials for food, feed and energy were collected, fermentation protocols were developed and applied at laboratory scale for different materials, and methods for analysing contents of antinutrients and bioactive compounds were established. These will be optimized in laboratory-scale, after which they will be transferred to a large-scale process for further optimization.
The readiness to produce selected micro-organisms in a bioreactor was established. Also, for cryopreservation of desired microbes and microbial consortia as starters for the needs of process industry, collection of data and organizing laboratory facilities were carried out. Collection of protocols to be used for rapid identification of microbes was carried out.
A SIMBA project clinical trial, along with earlier studies, was conducted to find how sustainable diet and fermented products effect human health and gut. The clinical trial was carried out, with participants consuming 5 grams/day of fermented seaweed and canola, or a rye cereal placebo. To study the effect of plant-based diets on human gut microbiota and health, stool, urine and blood samples were analysed with mass spectrometry-based methods to analyse polyphenol metabolites and bile acids.
A key objective of the SIMBA project is to bring microbial applications to the market that assist food chain.Value chain scenarios were identified and described for four food products: potato, wheat, tomato, and fish reared with feed recovered from algae. To find the barriers and drivers of uptake of microbial innovations by farmers and consumers a literature study was conducted and surveys were developed for three arable crops and were distributed online in five languages (English, Dutch, German, Italian, Finnish). Additional questions on COVID-19 were included in the questionnaires to evaluate the effect of the ongoing pandemic on the willingness of farmers/consumers to adopt/buy microbial applications/food products. The results of the data analyses from the surveys and recommendations will be available by November 2020.
• Open access central database containing microbiome data that facilitate the identification of potentially useful microbes or groups of interacting microbes that have useful function in the food production process.
• Enhanced consistency of microbiomes in field applications through the identification of best mixtures of plant growth-promoting microorganisms and bio-active compounds.
• Improved understanding of the role of salt-tolerant microbiomes and their role in the cultivation of salt resistant crops, contributing to the reclaiming of land lost to desertification and increasing arable land.
• Starter cultures to be applied in food products with beneficial compounds, contributing to health human benefits.
• Improved understanding of the functions of individual and sustainable diet-induced variations in gut microbiota, and their interaction with diet and foods, which is expected to contribute to the prevention of certain chronic diseases, such as Type 2 diabetes.
• Near to market ready development of new and cost-effective applications, products and services of new microbes, food, crop and algae products through upscaling from laboratory to pilot scale processes.
• Proven increase in sustainability of European food systems by implementing the microbial interventions.
Potential impacts
• Knowledge and applications of terrestrial, marine, and food driven microbiomes to increase productivity, quality, safety, sustainability and nutrition security in the food chain
• Nutrition security can be better ensured adopting a food system approach based on sustainability, linking land and sea and encompassing the entire food value chain
• Public and private food system stakeholders can increase their innovation capacities and facilitate their access to contemporary scientific knowledge