HoloFood

    HoloFood - Unlocking a Holo-Omic framework for food production

    HoloFood is a 'hologenomic' approach that will improve the efficiency of food production systems by understanding the biomolecular and physiological processes affected by incorporating feed additives and 
novel sustainable feeds in farmed animals.  

    The HoloFood consortium will showcase the potential of an innovative solution that holds enormous potential for optimising modern food production. Specifically, HoloFood is a framework that integrates a suite of recent analytical and technological developments, that is applicable to any major animal food production system, spanning the full production line


    Thus it is as relevant for the farmers producing livestock, as it is to the associate industries such as those producing the feed and feed additives upon which the animal’s growth, quality, health and wellbeing depends. 

    HoloFood is a Horizon2020 Innovation Action, comprising of 10 organisations from across Europe

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    The Challenge

    With the planet’s population rapidly increasing, one of the key global challenges of this century is to secure that the growing food production is performed in a sustainable fashion and with a low-carbon signature. 
    Optimising food production is thus not only of commercial interest for companies, but also of critical importance for humanity. 

    It is well known that gut microorganisms play a pivotal role in the health and growth of animals, and a balanced gut microbiota is essential for an optimal food production.

     In the last decades, and in particular since the 2006 ban of using antibiotics to promote animal growth in the European Union, different strategies are being developed to modulate gut microbiomes aiming to improve food production, such as functional feed components or feed additives.

    Feed additives have been proven effective at modulating microbiomes in many animal systems, although 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


    Understanding the effect of these additives is poorly understood, because the microorganisms of interest might interact with hundreds of other microbial taxa as well as the host organism. 
    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. 

    The HoloFood Concept

    The holo-omic approach considers the holobiont (host animal and its associated microbiota) as a single unit of action, across multiple molecular levels.


    ​To achieve this, we take advantage of a wealth of new developments in affordable analytical tools, in order to understand key metabolic interactions between not only the host animal’s genome, but also its transcriptome, and its microbial metagenome and metatranscriptome. Moving beyond just genetic data, the framework also incorporates accessory information from associated (meta)metabolomic and immune response information, so as to fully recover the functional pathways controlling the host phenotype. 


    Therefore in the context of the effect of feed on animal production, this approach enables us to move beyond simply showing that feed affects a host’s phenotype (whether growth, quality, health, welfare or even gut microbiome community structure), to actually understanding how the feed, host and microbes interact to yield the phenotypes.


    The Hologenome concept : The host and it's respective microbiome interact with each other Figure from Limborg M. et al 2018 (https://doi.org/10.1016/j.tibtech.2017.12.006)
    Biomolecular interactions between hosts (animals) and their respective microbiomes are triggered by environmental factors and yield very different results for each host (Figure from Limborg et al 2018 https://doi.org/10.1016/j.tibtech.2017.12.006)

    The Solution

    In HoloFood we will use 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 feed and food production. We will achieve this through implementing a novel holistic framework, namely the holo-omic framework, that principally exploits decreases in sequencing costs, coupled with cutting-edge biomolecular and statistical methods.


    The holo-omic framework aims to characterize not only an animals’ associated gut microorganisms’ whole genomes, transcriptomes and metabolomes, but also their genomes, intestinal transcriptomes and intestinal immune processes, all in relation to production performance parameters and animal welfare.

    Our Objectives

    HoloFood’s overall objective is to implement a timely technological solution based on cutting-edge biomolecular research in the food industry, which will:

    1.  Optimise animal food production systems by improving different stages of the production line.

    2.  Showcase the benefits of understanding the feed-microbiome-animal interactions through the application of state-of-the-art scientific methods to the food production sector and the general public.

    Raise awareness

    ...of microbiome modulation approaches to improve food production systems, disseminate key results and train relevant users 

    Advance the holo-omic framework

    ... to increase efficiency and versatility to ensure applicability on a wider range of production environments and food production chain steps. 

    Identify host - microbiota interactions

    ... that relate to feeds and feed additives with production parameters of interest. 

    Generate a Holo-Omic database

    ... containing feed-host associated microbiota biomolecular information linked to production parameters of interest.

    Design new strategies

    ...to optimise feeding and feed additive

     administration strategies, decreasing our reliance on unsustainable food production practices. 

    Pilot in commercial environments

    ... validation through piloting under commercial production scale environments in poultry and aquaculture.

    Evaluate the commercial and social impact of the HoloFood solution


    HoloFood Animal Models

    We will use two critically important farmed animal systems as our models – salmon and chicken – and use the newly developed holo-omic framework to characterize not only their associated gut microorganisms’ whole genomes, transcriptomes and metabolomes, but also their genomes, intestinal transcriptomes and intestinal immune processes, all in relation to production performance parameters and animal welfare. 

    Chicken Trials

    HoloFood will analyse the impact of the interactions between feed additives (probiotic and prebiotic), gut microorganisms and host animals over relevant performance parameters, under three different commercially relevant feeding regimes.

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    Salmon Trials

    HoloFood will experiment with a novel functional feed component, (seaweed), and a novel protein source as a new sustainable alternative to fish meal. 

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    Our Targets

    The knowledge generated will be used to optimise the feed additive strategies implemented in food production, by tailoring them to the genetic background and developmental stage of the animals, as well as production environment.


     In doing so we will improve the quantityquality and safety of the produced food, as well as increase the sustainability of food production and animal welfare

    The ambition of the HoloFood solution is to create a versatile framework that can be applied in theory to any food production system that relies on the co-interaction of animals and their gut microorganisms.