HoloFoodR: A statistical programming framework for holo-omics data integration workflow

Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10 000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. To address it, we introduce HoloFoodR, an R/Bioconductor package, which streamlines access to the HoloFood database. The retrieved data is available in MultiAssayExperiment and TreeSummarizedExperiment formats, enabling simple access to downstream analyses using thousands of packages from the R/Bioconductor ecosystem. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

Presented at the European Bioconductor Conference (EuroBioC2026), Turku, June 2026