Fig. 2

16S rRNA Gene profiling of the gut microbiome across feeding type and intestinal sections. A For the mid and distal gut sections separately, the barplots show relative abundance of high abundant bacteria defined as being present in more than 2% of all samples. B Principal Coordinates Analysis (PCoA) of the microbial composition in all samples and feeding groups using Unifrac distances. Distribution of individual samples for the three feeding groups are plotted for the same axes but shown in separate plots for visual purposes. Grouping of rainbow trout reared on different feeding types were visualised as orange for CTRL, blue for PRO, and red for SYN. Shapes indicate different intestinal sections, where the circle indicates samples isolated from distal gut content and triangles indicate samples isolated from mid gut content. C–E Boxplots of effective numbers of ASVs (Hill numbers) of microbiome across feeding types, including CTRL, PRO, and SYN. Order of effective numbers include C ASV Richness, q = 0, D ASV Shannon diversity (q = 1), E ASV Simpson diversity (q = 2). Significance code: [ns] > α = 0.05; [•] < α = 0.1; [*] < α = 0.05; [**] < α = 0.01; [***] < α = 0.001; [****] < α = 0.0001. F Heat Tree of species composition of the 50 most abundant ASVs throughout the gut combined with pairwise comparisons for the three feeding types, CTRL, PRO, and SYN. The grey tree on the lower left is a taxonomic reference for the smaller unlabelled trees. The most abundant genera from figure A are coloured in red and underlined. The colour of each taxon reflects differential abundance between the two groups being compared with colours determined by the log2 ratio of median proportions of reads observed in each feeding type. The Log₂ changes were determined using a Wilcoxon rank-sum test followed by a Benjamini-Hochberg (FDR) correction for multiple comparisons. The size of nodes relates to the number of ASVs found within the given taxonomic group