Projects

 

MASTER- Microbiome Applications for Sustainable food systems through Technologies and EnteRprise

The overall aim of MASTER - more Info go to the Website 1- 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 2, 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.

Website MASTER 3

 

Microbial population interactions in the cow’s rumen

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. 

Webpage 4

 

The HDHL-INTIMIC (Healthy Diet for a Healthy Life - INtesTInal MICrobiomics) Knowledge Platform on Food, Diet, Intestinal Microbiomics and Human Health

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.

Webpage 5