Supporting the development of hologenomic approaches for more sustainable animal feeds

Credit: Karen Arnott/EMBL-EBI using stock imagery from Anttoniart/stock.adobe.com and Inna/stock.adobe.com


  • Chicken and salmon are two major sources of protein.
  • More sustainable feed alternatives would reduce the environmental impact of animal production and improve food security. 
  • The HoloFood project has published the most comprehensive biomolecular dataset exploring how microbes in the chicken and salmon guts may be altered by different types of feed. The data is useful for developing better animal feed.  

Meat production is one of the most resource-intensive industries. Among other things, the feed that animals consume needs to be nutritious and sustainable

The HoloFood project, funded by Horizon 2020, has been taking a closer look at the relationship between farmed animals, the food they eat, and the microbes living in their guts, focusing in particular on chicken and salmon. The aim of the project is to support the development of more sustainable animal feed.

After four years of data collection, the project has launched the HoloFood Data Portal. This is the world’s first freely-accessible database containing comprehensive biomolecular data that enables researchers to understand the microbial diversity in the chicken and salmon gut, and how changes in diet affect animal health. “The HoloFood project has identified sustainable feed alternatives, for example, naturally growing blue mussels, which can be an alternative to fishmeal that typically comes from forage fish, such as anchovies and herring, and has caused the collapse of some populations,” explained Rob Finn, Team Leader at EMBL’s European Bioinformatics Institute. “But this is only the beginning. The potential of this dataset is massive for animal feed companies, as we begin to understand the complex molecular relationships between feed, environment, microbiome, and animal.”

Credit: HoloFood Consortium

Supporting a new scientific field

The project leveraged an emerging scientific concept called hologenomics, which analyses as a single unit the host animal and its many molecular layers, including the microbes living in and interacting with it. A collection of such species that interact among each other is called a holobiont. 

Through close monitoring, the researchers collected an unparalleled wealth of data from salmon and chicken. This includes host animal genomes, metagenomes, metabolomes, and phenotypic data, among others.

Using these datasets, researchers can explore how different types of feed might affect the animals’ microbiome, growth, immune response, and meat quality. The data are now openly-available through the HoloFood Data Portal, and researchers around the world can use them to ask in-depth questions and gain new insights. 

“We know that bacteria living in the gut can play a pivotal role in animal health and growth, but the details of microbe functions and interactions are complex, ” explained Varsha Kale, Bioinformatician at EMBL-EBI. “The HoloFood project has explored this in more detail than ever before, making the data and findings openly available to the global scientific community. We have shown the potential of using the gut microbiome to investigate more sustainable and cost-effective animal feeds, and we hope other researchers and companies will continue this work worldwide.” 

Caption: Graphic showing the pairwise relationships between samples available in the HoloFood Data Portal. Each link shows a combination of two samples from the same animal, which form the basis of multiomic analysis. Credit: HoloFood Consortium

The first portal of its kind

“The value of the HoloFood Data Portal lies in its interconnectivity and the broad range of data available,” explained Alexander Rogers, Developer at EMBL-EBI. “Because the data are high-quality and have been painstakingly annotated, they are perfect for developing new tools and algorithms that allow researchers to gain a better understanding of creatures in their environment – within food production and beyond.”

The HoloFood Data Portal is the first of its kind and can serve as a model for sharing other holobiont datasets. 

One of the projects that is already taking advantage of the HoloFood Portal to improve knowledge of host-microbiome interaction is FindingPheno, which is also funded by the European Union’s Horizon 2020.

Decades of data management expertise

The HoloFood consortium consists of 11 partners across 6 countries. This includes EMBL’s European Bioinformatics Institute (EMBL-EBI), near Cambridge, UK. 

Building on its 30 years of data management expertise, EMBL-EBI contributed data curation and annotation expertise, and the development of the HoloFood Data Portal. The portal’s user-friendly interface is easy to navigate and search by metadata (for example, phenotypes such as breed, age, etc.), sample, or treatment. 

HoloFood is one of many initiatives undertaken as part of EMBL’s Microbial Ecosystems transversal theme, which aims to explore microorganisms and their interactions with each other and with their environments.


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

Tags: big data, bioinformatics, data, data science, data service, data sharing, database, embl-ebi, FAIR data, genomics, industry, microbial ecosystems, microbiome, open data, sustainability


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