Microorganisms make up a large part of the total biodiversity on our planet and often flow between ecosystems. In today's agricultural and food production systems, they are of tremendous importance as they can, for example, improve the smell or taste of food products or lead to spoilage. In the Micro-Tramper project, we want to understand microbial flows along the food production chain. To do so, we work hand in hand with five Austrian higher education institutions that focus on agriculture, nutrition or food production. The scientific goal is to sequence genomes of relevant microbes in food production and to decode the function of microbial genes in the ripening process of food.

Students taking part in the project will collect samples from family-owned facilities that are active in food production, hand-made cheeses at different times of ripening, their home kitchen and themselves.

From these samples, they extract deoxyribonucleic acids (DNA) and use sequencing to study the microbial composition or ‘microbiome’. This is done under the scientific guidance of university researchers and will employ some of the latest developments in DNA sequencing. A MinION device from Oxford Nanopore Technologies, which is small and flexible, will be used to conduct sequencing at the schools. Data processing and analysis will also take place at the schools where it can be compared and interpreted together with the students. Lastly, teachers at the partner schools will be trained to be able to conduct sequencing projects on their own in the future. Communication workshops are intended to encourage students to share their research and present it at various events, including online micro-parties and micro-flash mobs. In addition, a song about the importance of preserving microbial diversity will be created. Based on the collected data, students will be able to i.) evaluate the established hygiene measures and discuss improvements for their family facilities, ii.) re-think food loss in their own household and reduce it together with the family and iii.) better use disinfection as a hygiene measure. Students can then recognize the importance of microbial diversity, understand challenges posed by microbial flows along the food production chain and be well-prepared for the use of hygiene measures.

The scientific value of this project lies in the detection of microbial genes that are essential for resilience and toxicity in farms, as well as in understanding microbial interaction in ripening processes of fermented food. Building on the existing curricula, the MinION sequencers acquired through the project should expand the possibilities for schools to integrate practical research in their teaching and generate interest about microbiome science among teachers and students. Even after the end of the project, the sequencers will remain in the schools for continued use in the classroom. Further, the partner schools will connect and stay in contact well beyond the duration of the project.

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The overall aim of MASTER is to take a global approach to the development of concrete microbiome products, foods/feeds, services or processes with high commercial potential, which will benefit society through improving the quantity, quality and safety of food, across multiple food chains.

For this project, we visit food-producing facilities, collect samples, do nucleic acid extraction for high-throughput sequencing and subsequent bioinformatics analysis and develop software and pipelines for the analysis of such data. This is the case for the already published TORMES pipeline of our postdoc Narciso Martin Quijada Website, that was initially developed in the “Instituto Tecnológico Agrario de Castilla y León” (Valladolid, Spain) in collaboration with the University of Burgos (UBU, Spain) and the “Hospital Universitario Río Hortega” (Valladolid, Spain).

TORMES allows, with the use of very simple instructions, to perform the complete analysis of bacterial genomes obtained by whole genome sequencing directly from the raw sequencing data, with special focus on antimicrobial resistances.

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Rumen microbial ecology has been intensively studied, from the pioneering cultivation efforts by Robert Hungate to the recent establishment of comprehensive metagenome-assembled genome (MAG) databases. However, this work has focused on the rumen content whereas the rumen epithelial wall, especially in terms of cultivation, has been comparatively neglected.

Interestingly, multiple 16S rRNA amplicon datasets from the rumen epithelium have found a single ASV affiliated with the Campylobacteraeceae to be extremely dominant (1-30% relative abundance). Here, we collected metagenomes from epithelial samples, recovered 3 MAGs, and found that the 2 most abundant of these fall into a clade of Campylobacteraeceae distantly related to the classical Campylobacter pathogens (C. jejuni and C. coli). Fortunately, we were able to cultivate and sequence the genomes from >30 representatives and show that they represent two highly differentiated populations. By applying a reverse ecology approach, we have been testing hypotheses about how these two populations, and the gene flow units within them, map onto different ecological roles. Our hope is to provide a solid basis for understanding whether these microbes influence animal health. 

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HDHL-INTIMIC aims to coordinate national and regional programmes in the area of diet, intestinal microbiomics and health as well as nutrition and health in general, thereby contributing to the implementation of JPI HDHL (The Joint Programming Initiative - a Healthy Diet for a Healthy Life) objectives. In the programme, 26 countries from within and outside of Europe are working on a programmed approach to align national R&I strategies and to fund new research, in order to facilitate true understanding of the relationship between diet, physical activity and health.

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