HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production

Abstract

The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.

Figure 1.

The schema used for HoloFood animals and samples registered in BioSamples [8]. Individual animals are accessed as BioSamples, with metadata sections as shown on the left. Most of these metadata sections are shared between the two systems. Extraction-level (derived) samples are registered separately in BioSamples, and BioSamples relationships are used to connect each derived sample to its parent animal-level sample. Metadata are also available on the derived samples, which include the experimental results for assays like fatty acid measurements in salmon and inflammatory markers in chicken. Analysis results for the derived samples are stored in the most appropriate repository, as indicated by the service icons alongside each type.

Figure 2.

Genome catalogues were created for each system. HoloFood-derived metagenome-assembled genomes were combined with other publicly available chicken and fish data to produce genome catalogues for the MGnify Genomes resource [11]. In this example, the HoloFood genome clusters with three other genomes at the species level. This genome is best represented by a non-HoloFood representative. The data portal lists the HoloFood-derived genomes, with links to the best cluster representative for each species, for which annotations can be browsed on MGnify.

Figure 3.

Overview of the multiomic samples available in the HoloFood Data Portal for each system. Different multiomics sample sets were extracted from animals in multiple trials and time points. Each row shows how many individual animals are available covering that multi-omic combination. Combinations are shown where at least five individuals are available (which excludes eight chickens and two salmon). ‘Phenotype’ encompasses several experiment types: inflammatory markers, histology, fatty acids, iodine, and heavy metals; half of the 433 salmon with only phenotypic data have more than one phenotypic sample type.

Figure 4.

The primary dataset available in the data portal is a list of samples (registered in BioSamples). The sample list (in the background of this composite screenshot) can be partitioned along different axes: in this case by system, omic type, and treatment. It can also be partitioned by host, as shown by the inset which shows the content of a salmon detail page linking to five derived omics samples. Animals (which are also represented by a BioSamples identifier) can be similarly listed and the hierarchical relationship between samples and animals can be used to navigate and filter the data. The same filters and lists can be used programmatically via the API.

Figure 5.

Screenshot showing a sample detail page for a metagenomic sample (left). The analysis of metagenomic samples is performed by and stored in MGnify [9]. The data portal shows a summary of this MGnify data and links to MGnify where users can browse the analysis dataset (right).