Effects of dietary inulin and Ichthyophthirius multifiliis  (Ich) infection on the gill transcriptome in zebrafish
Infection was the dominant driver of host transcriptional responses in the gills, inducing widespread differential gene expression associated with innate immunity, epithelial barrier function, ribosome biogenesis, proteasome activity, and cellular stress responses, while suppressing pathways linked to growth, signalling, and tissue homeostasis. Inulin had comparatively (and expectedly)  modest transcriptomic effects, yet diet-associated gene regulation was evident, and infected inulin-fed fish displayed strong up-regulation of immune and barrier-associated genes Overall design: To examine whether diet-induced changes in the zebrafish gut microbiome influenced zebrafish susceptibility to I. multifiliis and subsequent host-parasite interactions, we utilised 4 groups of 30 adult AB wildtype zebrafish (Fig. 1). Two of the groups (n = 60) were given a control diet whilst the two other groups (n = 60) were given the same diet supplemented with 20% inulin. One group from each diet (n = 2 × 30) was infected with 4000 I. multifiliis per fish after 35 days of diet intervention. The other group from each diet (n = 2 × 30) was a non-infected control. The fish were euthanised after 5 days of infection, and a subset of samples (37) were used for RNA-Seq.