Feed microbiome: confounding factor affecting fish gut microbiome studies.

There is an increasing interest in the impact of feed on the fish gut microbiome. Most of the studies are based on sequencing the bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well as dead bacteria. It has not been a common practice to include the feed as control, although it contains various nutritious ingredients that microorganisms can use before or after feed preparation. Thus, study designs using digesta as a proxy for the intestinal microbiome raise the concern that composition of the gut microbiome might be biased by carry-over of microbial DNA from the feed itself. Here we report analysis of 15 feeds and representative intestinal digesta of Atlantic salmon (Salmo salar) from five independent case studies. This allowed us to identify "feed microbiomes" that were microbially diverse and shared taxa with digesta microbiomes. Digesta-specific microbiomes were identified, though they were mainly enriched by a few taxa, such as Mycoplasma and Ruminococcaceae. Overall, findings are consistent with a model wherein gut microbial profiles are to a different degree influenced by bacterial DNA present in the feed itself through a "feed microbiome" carry-over effect.

Responses to Mineral Supplementation and Salmon Lice (Lepeophtheirus salmonis) Infestation in Skin Layers of Atlantic Salmon (Salmo salar L.).

The crustacean ectoparasite salmon louse (Lepeophtheirus salmonis), which severely affects Atlantic salmon health and welfare is one of the main problems of commercial aquaculture. In the present study, fish were fed a diet supplemented with extra minerals through the inclusion of a commercial additive (Biofeed Forte Salmon), substituting wheat in the control diet, before experimental infestation with salmon lice. Lice counts reduced with time but with no apparent effect of the diets. Further, fish fed the mineral diet had an overall higher number of blue (acidic) mucous cells, while the ratio of purple mucous cells was higher in the mineral diet. The transcriptional response in skin was enhanced at 7 dpc (copepodite life stage) in fish fed the mineral diet including immune and stress responses, while at 21 dpc (pre-adult life stage), the difference disappeared, or reversed with stronger induction in the control diet. Overall, 9.3% of the genes affected with lice also responded to the feed, with marked differences in outer (scale + epidermis) and inner (dermis) skin layers. A comparison of transcriptome data with five datasets from previous trials revealed common features and gene markers of responses to lice, stress, and mechanically induced wounds. Results suggested a prevalence of generic responses in wounded skin and lice-infected salmon.