HoloFood Scientific Publications

Here you can find academic publications resulting from HoloFood research

Research Article: 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

Figure from Duangnumsawang et al. (2023) Veterinary Research Communications

Research Article: 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

Figure from Eisenhofer, Odriozola & Alberdi (2023) ISME Communications

Research Article: 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

Research Article: 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

Research Article: 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

Figure from Tous et al. (2022) Frontiers in Physiology

Research Article: 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 Advanced Genetics here: https://doi.org/10.1002/ggn2.202100065

Research Article: 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

Figure from Brealey et al. (2022) ASM Journals. mBio

Review: Disentangling host–microbiota complexity through hologenomics

A review article in the journal Nature Review Genetics by HoloFood coordinators Tom Gilbert, Antton Alberdi and Morten Limborg was 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

Figure from Alberdi et al. (2022) Nature Reviews Genetics

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

Figure from Duangnumsawang, Zentek & Boroojeni (2021) Frontiers in Immunology

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.

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

Figure from Bozzi et al. (2021) Animal Microbiome

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

Figure from Nyholm et al. (2020) iScience

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