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

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.

Growth and metabolic performance of house fly and black soldier fly larvae differ across densities and waste-based growth substrates.

Large scale production of insect larvae is considered a sustainable way to upcycle various organic waste- and by-products into more valuable food and feed products. The sustainability of insect larvae production depends on the substrates and species being used, but comparative studies that include both growth and efficiency are lacking. Here we compare larval fitness, including survival, development time, weight, substrate conversion efficiency, substrate reduction, and metabolic parameters across different combinations of densities and waste- and by-product-based substrates on the two fly species, the house fly (Musca domestica) and the black soldier fly (Hermetia illucens).

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production.

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.

Intestinal microbial profiles of wild Alaskan rainbow trout () characterized by 16S rRNA amplicon data.

Rainbow trout () is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA.