(A) Cluster analysis of gut RNA-Seq from intestines from 6-week-old fish (6wk) and 16-week-old fish (16wk, Omt (red) and Ymt (green)). (B) Expression heatmap for the 80 top differentially expressed genes (DEGs) between Ymt and Omt fish (n = 4 for each group). *HAMP is the best protein blast hit in Danio rerio of the TK gene NFURG05812010005 (Figure 7—source data 1). (C) Gene Ontology (GO) analysis of the DEGs between Ymt and Omt fish. Enrichment values (bars) and the negative natural logarithm of p values (black dots) are shown. Endonuclease activity* indicates the following GO function: ‘Endonuclease activity, active either with ribo or deoxyribonucleic acids and producing 3’ phosphomonoesters’. (D) Relative gene expression levels compared to 6-week-old fish (6wk) of genes significantly differentially expressed between 16wk (gray), Omt (red) and 6wk (black), but not between Ymt (green) and 6wk. These genes are also significantly differentially expressed between 16wk and Ymt. (E) Based on the correlation matrix between OTU abundance and transcript levels in individual fish (Figure 7—source data 2), we identified the gene transcripts whose expression correlates more significantly with the hub bacteria shared between Ymt and 6wk fish (full analysis in Figure 7—figure supplement 2). Displayed are the top hits (chosen from an r-square value larger than 0.65 on both axes) shared between Psychrobacter and Exiguobacterium, which have the highest OTU-transcript correlation trend based on Figure 7—figure supplement 2. RPLs include RPL7A, RPL8, RPL12, RPL37, RPL14, MRPL35; while RPS include RPS3A, RPS7, RPS11, RPS24.