HoloFood
    Public Article

    World Microbiome Day: Open access HoloFood Data Portal can help create more sustainable animal feeds

    Article in Nutrition Insight about the HoloFood data portal and its uses for sustainable animal feeds.

    Link here: https://www.nutritioninsight.com/news/world-microbiome-day-open-access-holofood-data-portal-can-help-create-more-sustainable-animal-feeds.html                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         

    HoloFood resource

    HoloFood Data Portal

    HoloFood partner EMBL-EBI have released the HoloFood data portal - a valuable resource for research and industry stakeholders interested in further exploring the salmon and chicken data generated from the project.


    Read the relevant article news story here:

    https://www.ebi.ac.uk/about/news/technology-and-innovation/holo-food-data-portal/


    Or check out our behind the scenes blog here:  https://www.holofood.eu/blogs/post/blog-takeover-embl-ebi                                                                                                                                                                                                                                                                                                                                                                                      

    Scientific Publication

    Impact of feed additives and host-related factors on bacterial metabolites, mucosal integrity and immune response in the ileum of broilers

    HoloFood partners from the Freie University of Berlin (PhD student Yada Duangnumsawang, Prof. Jürgen Zentek, Dr. Wilfried Vahjen and Dr. Farshad Goodarzi Boroojeni) together with Joan Tarradas (IRTA) published a peer reviewed article aimed to investigate the effect of age, breed, and sex of chicken broilers, as well as a probiotic or phytobiotic product on mucosal morphology, bacterial metabolites, and immune traits in the ileum of broilers.


    You can read the full article in Veterinary Research Communications here: https://doi.org/10.1007/s11259-023-10135-9                                                                                                                                                                                                                                                                                                                                                                                                                                                                           

    Public Article
    Cover of special issue in Kaskelot. Photo courtesy of Biologiforbundet

    Special issue on hologenomics in Kaskelot magazine

    HoloFood scientific manager Morten Limborg wrote an article in the danish public science publication "Kaskelot" on the applied aspects of hologenomics within aquaculture and food production, highlighting amongst others the outcomes of the HoloFood project. The article is in Danish and distributed across Denmark, aimed at educators and those interested in science.


    Further details on the special issue as well as useful resources can be found here.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        

    Scientific Publication

    Impact of microbial genome completeness on metagenomic functional inference

    Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this overlooked bias in metagenomic functional inference.

    You can read the full article in ISME Communications here: https://doi.org/10.1038/s43705-023-00221-z                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             

    Scientific Publication

    Alterations in bacterial metabolites, cytokines, and mucosal integrity in the caecum of broilers caused by feed additives and host-related factors

    Results of the metabolic profiles from the HoloFood chicken trials are outlined focusing on the impact of age and diet. The results showed that bacterial metabolites could play a significant role in mucosal development and immunological response in the caecum of broilers.

    You can read the full article in Frontiers in Physiology here: https://doi.org/10.3389/fphys.2022.935870                                                                                                                                                                                                                                                               

    Scientific Publication

    A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis

    Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host–microbe–microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. We present one of the first models able to describe a, albeit simple, complete intestinal microbiome community of a vertebrate host. Our model stands out from predecessors by considering realistic parameters of the host immune function, a mutualist microbe able to induce host immune reactions, and a toxin-producing pathogenic microbe.

    You can read the full article in Frontiers in Microbiology Journal 

    doi: 10.3389/fmicb.2022.912806                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
    Scientific Publication

    Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics

    In this paper, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance.


    You can read the full article in Frontiers Journal here: https://doi.org/10.1002/ggn2.202100065                                                                                                                                                                                 

    Scientific Publication

    Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation

    A new research paper from HoloFood provides a 2  step approach to generate high quality host genomes from shotgun metagenomic datasets. This method allows researchers to utilise host DNA from metagenomic runs and impute genetic structure from host populations. 


    You can read the full article in Advance Genetics here: https://doi.org/10.1002/ggn2.202100065       
                                                                

    Public Article

    "A holistic view of the organism and its microorganisms" - public article in Danish

    Danish magazine Aktuel Naturvidenskab featured the HoloFood project in a recent article highlighting hologenomics. The article focuses on sustainable aquaculture as an example to communicate the science behind hologenomics to their audience.


    You can read the full article in Danish here:   https://aktuelnaturvidenskab.dk/find-artikel/nyeste-numre/3-2022/et-holistisk-syn-paa-organismen-og-dens-mikroorganismer               

    Public Article

    European Aquaculture Society March edition magazine

    HoloFood was briefly mentioned as being at the forefront of salmon aquaculture hologenomics aiming sustainable feed solutions.

    Building the industry-academia relationship is key to the future success of building a scientifically-informed future for aquaculture.

    The article can be found here:  https://www.aquaeas.eu/publications-new/eas-magazine              
                                                 

    Scientific Publication

    Microbiome “Inception”: an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host

    A new research article on endoparasite - host relationship in salmon by HoloFood researchers is published in mBio with some surprising insights. The results suggest that parasit cestodes may be themselves holobionts within the microbiomes of their fish host - emphasizing the importance of also considering microbes associated with parasites when studying instestinal parasitic infections. 


    You can read the full paper here:   https://doi.org/10.1128/mbio.00679-22

    Scientific Publication

    Review: Disentangling host–microbiota complexity through hologenomics

    A new review article in the journal Nature Review Genetics by HoloFood coordinators Tom Gilbert, Antton Alberdi and Morten Limborg is published. The review covers the field of hologenomics, the advantages and current limitations of such studies and how best to design a hologenomic research project. 


    You can read the full paper here: https://doi.org/10.1038/s41576-021-00421-0

    Scientific Publication

    Review: Development and Functional Properties of Intestinal Mucus Layer in Poultry

    A new review article in the journal Frontiers in Immunology by PhD student Yada Duangnumsawang, Prof. Jürgen Zentek and Dr. Farshad Goodarzi Boroojeni from Freie Universität Berlin, explores the importance of the intestinal mucus in the poultry gut. The mucosal barrier of the gut is the first line of defence against the invasion of pathogens, supporting the colonization of beneficial bacteria and maintaining the proper environment for digestion. In spite of its great importance, little is known about the structure and functional properties of the intestinal mucus layer within the chicken gut. This review expands on our current understanding of this important intestinal mucus, the impact of age on the development of the cells that are a part of it as well as the dietary factors that impact them. 


    You can read the full paper here: https://doi.org/10.3389/fimmu.2021.745849

    Scientific Publication
    salmon health hologenomics

    Research Article: Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

    MSc student Davide Bozzi and researchers and industry partners from the HoloFood project have published a new research article on monitoring salmon health in response to disease and treatment to disease within aquaculture. The study, entitled 'Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals' was published in Animal Microbiome Journal, and was a collaborative effort between academic and industry partners of the consortium. 


    Read the behind the behind-the-paper blog by clicking here 

    Or access the full paper: https://doi.org/10.1186/s42523-021-00096-2        


    Scientific Publication

    Perspective Article: Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research 

    PhD student Lasse Nyholm Jessen and his colleagues from the HoloFood EU project and Center for Evolutionary Hologenomics at University of Copenhagen have published a perspective paper on the new possibilities of holo-omics in the open access journal iScience.


    Read the relevant news article : https://ceh.ku.dk/news/2020/the-holo-omic-approach-opens-up-new-research-avenues/


    Read more in the original open access paper: https://doi.org/10.1016/j.isci.2020.101414

    Article featuring HoloFood's activity in Horizon Magazine 

    This project has received funding from the European Unionʼs Horizon 2020 research and innovation programme under grant agreement No 817729


    Project Coordinator: Prof. Tom Gilbert -  University of Copenhagen

    Scientific Managers : Associate Professors Antton Alberdi and Morten Limborg University of Copenhagen    

                                                 

                                                                                                                                     

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    CONTACT : holofood@ku.dk

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