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Holistic solution to improve animal food production through deconstructing the biomolecular interactions between feed, gut microorganisms and animals in relation to performance parameters

Periodic Reporting for period 1 - HoloFood (Holistic solution to improve animal food production through deconstructing the biomolecular interactions between feed, gut microorganisms and animals in relation to performance parameters)

Reporting period: 2019-01-01 to 2020-06-30

With the continuous increase in human population, one of the key global challenges is to secure that the necessary growing food production is performed sustainably. It is known that gut microorganisms play a pivotal role in the health and well-being of animals, and a balanced gut microbiota is essential for optimal food production. In the past, different strategies are being developed to modulate gut microbiomes aiming to improve food production. Feed additives have been proven effective at modulating microbiomes in many animal systems, although both producers scientific data confirm that their efficiency often exhibits large variation. The likely reason underlying such inconsistency is the very limited knowledge we have about the specific means of action of the additives. In the best case, feed additive or food producing companies might employ both in vitro and in vivo experiments to test the properties and benefits of the additive. However, the information capacity of these approaches is limited, as the in vivo response of microorganisms can be radically different from in vitro conditions, because the microorganisms of interest are under different physico-chemical conditions and might interact with hundreds of other microbial taxa as well as the host organism. Thus currently, the improvement of feed additives usually relies on rudimentary trial-error in which researchers are unable to gain a full understanding of the reasons behind the success or failure of the use of different additives. Consequently, the procedures to improve the feed additive products are inefficient, and it is unlikely that any truly optimal product can be found without drastically modifying the approach taken. HoloFood is overcoming these limitations by leveraging state-of-the-art laboratory and computational developments, to provide direct insights into the effects of the biomolecular interactions between feed additives, gut microorganisms and host animals in food production. This is being achieved by implementing a novel holo-omic framework, that principally exploits decreases in the price of generating ‘omic datasets, coupled with cutting-edge biomolecular and statistical methods. HoloFood is based on two observations:i) Animals and their associated microorganisms behave differently depending on the environment and developmental stage of the animal and ii) many biological processes of animals and their associated microorganisms are affected, or even conditioned, by the other partner of the symbiosis. This implies that the effect of any feed additive could be different depending on the genomic background and developmental stage of the animal, microbiome composition, and the production environment. Our framework consists of analysing the genomes, transcriptomes and metabolomes of both animals and their associated gut microorganisms, then linking this to animal health and physiology, as well as food production performance parameters. To showcase the potential of our solution in different food production systems, and measure the commercial and societal impact of our approach, HoloFood will perform commercial-scale trials for both poultry and salmon in which the biomolecular interactions between microorganisms and animals fed with different feed additives will be analysed in relation to food production parameters measuring the quantity, quality and safety of the food, as well as the sustainability of food production and animal welfare. By understanding the physiological effects of the specific biomolecular interactions that occur when administering different feed additives, HoloFood aims to optimise their use by tailoring their administration to the genomic background and gut microbiome of the animals, as well as the farming environment, thus being able to increase the efficiency of feed additives and thereby improving final food products.In the future we believe that food production systems will be optimised through holo-omic approaches. Hence, HoloFood will act as a paradigm for approaches and in doing so foster the creation of jobs related to scientific research and the food sector, both directly with the production companies and associated industries. For achieving such ambitious goals, HoloFood brings together 11 partners from both academia and industry from 6 countries in Europe. Moreover, the activities of HoloFood will contribute towards achieving many of the challenges highlighted in the UN’s Sustainable Development Goals.
18 months since the project start, 10 deliverables have been submitted and 3 milestones have been achieved. In total there are 10 active work packages. As well as outcomes related to the project management in WP1(such as data management plan) and outreach and communication dissemination in WP2(such as the HoloFood website), we achieved important scientific results reported in the following work packages:
WP3 Design of the first draft of the HoloFood workbook that will be updated for the duration of the project.
WP4 Design, execution and near completion of experimental trials for both chicken and salmon.
WP5 Preliminary results regarding key performance indexes for chicken and salmon trials complete. Analysis of differences between experimental setups almost complete.
WP6 Setup of laboratory workflows and ongoing sample processing in laboratories in IMR, UCPH, FUB and AU. Preliminary sequencing underway. Preliminary genomic analysis of the different chicken breeds used in WP4. Curation and creating of data analysis pipelines and unique online repositories by EMBL-EBI for the datasets generated.
WP7 Ongoing phenotypic analysis of both chicken and salmon samples, with trial 1 for each animal almost complete.
WP8 Bibliographical revision and third party data gathering process has started.
WP9 Creation and curation of appropriate online depositories for all the different types of datasets generated by WP5,6 and 7 as well as creation of data analysis pipelines for analysis and integration of such datasets by EMBL-EBI.
The exploitation of the full potential of hologenomics within HoloFood requires a holistic analytical approach consisting of generating multi-omic data of both animals and their associated microbiota in relation to production parameters. In the first 18 months HoloFood has progressed through these targets. The design and implementation of large scale Holo-omic animal trials for both salmon and chicken farming and the information and data types collected from these provide a huge and unique resource not only for the objectives of HoloFood but for any future holo-omic study aiming to improve any other animal farmed system. All trial designs, laboratory and data generation protocols and data analysis pipelines and integrations so far created and executed are included into the HoloFood workbook, which at the end of the project will become public and can be utilised openly. The close collaboration of experts from all HoloFood beneficiaries, both from research institutions and industry partners means that the targets set out for the project are closely followed up on. This project goes beyond the state of the art as it introduces and implements the latest technologies and know-how and integrates interdisciplinary expertise across all work packages to achieve its goals. The innovation potential is thus fully exploited as the data is being generated thanks to the active and continuous communication between partners and work packages.