Additional file 1 of Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon
Creators: name: Schaal, Patrick
name: Cheaib, Bachar
name: Kaufmann, Joshka
name: Phillips, Karl
name: Ryder, Liz
name: McGinnity, Phil
name: Llewellyn, Martin
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology

description: Additional file 1: Table S1. Overview of the metabolic rate experiment. Sample_Id refers to individual fish. Sampling day refers to the day when fish were caught. Processing day refers to the day fish were dissected. Experiment day equals processing days, only in another format. Temperature refers to the water temperature at the sea pens on each sampling day. Table S2. First round PCR primers used for NGS library preparation. Table S3. Second round PCR primers used for NGS library preparation. Table S4. Mean length, weight and Fulton’s condition factor per genetic origin for 3 points in time (pre sea pen hatchery, date of sea pen transfer and at the termination point of the experiment). Table S5. ANCOVA results of the effect of AGD severity Score on weight adjusted SMR (left), MMR (middle) and AS (right) measures. Significance codes: *** &lt; 0.001; ** &lt; 0.01; * &lt; 0.05. Table S6. Multiple comparisons of means of metabolic rate measures between different AGD severity scores (Tukey post-hoc for weight-adjusted model). Significance codes: ** &lt; 0.01; * &lt; 0.05. Table S7. Permanova results showing differences between gut microbial community compositions of starved and fed fish for two different timepoints T0 and T1 in PC samples. Significance codes: ** &lt; 0.01; * &lt; 0.05. Table S8. Permanova results showing differences between gut microbial community compositions of starved and fed fish for two different timepoints T0 and T1 in MG samples. Significance codes: ** &lt; 0.01; * &lt; 0.05. Table S9. Linear model for Chao1 richness estimates in MG samples calculated by the interaction term of AGD severity score and genetic origin. AGD severity of 0 and farmed origin served as baseline for comparisons. Significance codes: *** &lt; 0.001; ** &lt; 0.01; * &lt; 0.05. Table S10. Permutational analysis of variance (PERMANOVA) results testing the effect of AGD severity score, genetic origin and processing day (day of gut dissection) on pyloric caeca (PC) microbial community composition based on weighted unifrac distance matrices. Table S11. Permanova of pairwise comparisons of PC samples grouped by day of their processing. Distance matrix calculated by weighted UniFrac measure. Permutations used: 9999. Significance codes: *** &lt; 0.001; ** &lt; 0.01; * &lt; 0.05. Table S12. Permutational analysis of variance (PERMANOVA) results testing the effect of AGD severity score, genetic origin and processing day (day of gut dissection) on midgut (MG) microbial community composition based on weighted unifrac distance matrices. Table S13. Permutational analysis of variance (PERMANOVA) testing pairwise comparisons for midgut (MG) samples from different AGD severity groups. Distance matrix calculated by weighted UniFrac measure. Permutations used: 9999. Significance codes: **p &lt; 0.01; *p &lt; 0.05.