Additional file 1 of Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater
Creators: name: Agboola, Jeleel O.
name: Rocha, Sérgio D. C.
name: Mensah, Dominic D.
name: Hansen, Jon Ø.
name: Øyås, Ove
name: Lapeña, David
name: Mydland, Liv T.
name: Arntzen, Magnus Ø.
name: Horn, Svein J.
name: Øverland, Margareth
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 1. Fig. S1. Rarefaction curves showing subsampling of sample into minimum sample sequence (1,604 sequence per sample). The rarefied amplicon sequence variants table was used for computation of Jaccard and unweighted Unifrac beta-diversity distances. FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Fig. S2. Principal component (PC) analysis on standardized amplicon sequence variants (ASVs). Score plots for PC1 and PC2 (A) and PC1 and PC3 (B), mean scores with 95% confidence intervals for PC1 (C), PC2 (D), and PC3 (E), and percentage of variance explained by PCs (F). FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Fig. S3. Principal component (PC) analysis on metabolic reaction abundances (z-scores). Score plots for PC1 and PC2 (A) and PC1 and PC3 (B), mean scores with 95% confidence intervals for PC1 (C), PC2 (D), and PC3 (E), and percentage of variance explained by PCs (F). FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Fig. S4. Expected (mock_exp) and observed (mock and mock_1) taxonomic profiles of the mock microbial community standard. Fig. S5. Microbiota composition of water samples. Relative abundance of the top 10 most abundant taxa at phylum level (A) and top 15 most abundant taxa at genus or lowest taxonomic rank (B). The mean relative abundance of each taxon within the same water type is displayed on the right side. The samples are group water type; SW – water collected from the source tank (i.e., header tank) and TW – water collected from the fish rearing tanks. Water collected from the 18 fish tanks were mixed, four subsamples were taken and used for the microbiota analysis. Fig. S6. Venn’s diagram (A and B) showing the shared and the unique amplicon sequence variants (ASVs) in the digesta sample of fish fed the experimental diets. The ASVs were computed using a prevalence threshold of 80%. FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Fig. S7. Boxplots for homogeneity of multivariate dispersions (PERMDISP) in gut microbiota of fish fed experimental diets. The PERMDISP test was based on; (A) Jaccard distance, (B) Unweighted Unifrac distance (C) Aitchison distance and (D) PhILR transformed Euclidean distance. The samples are grouped by diets; FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Fig. S8. Number of ASVs mapped to genome-scale metabolic models. Number of samples matched to models at different taxonomic levels (a) and the number of models mapped to each sample by taxonomic level (b). Fig. S9. The t-statistic tests comparing reaction abundances between each pair of diets. The t-statistic for each reaction is shown along with the mean across all reactions with 95% confidence interval for all significantly enriched subsystems. FM – fishmeal-based; SBM – soybean meal-based; 4 experimental diets containing 300 g/kg SBM and 100 g/kg of ICJ – inactivated Cyberlindnera jadinii; ACJ – autolyzed C. jadinii; IWA – inactivated Wickerhamomyces anomalus; AWA – autolyzed W. anomalus diets. Table S1. Composition of spray-dried yeasts with and without the autolysis treatment. All values are presented in % DM, except gross energy which is presented in MJ/kg DM. Table S4. Pair-wise comparisons alpha-diversity indices of gut microbiota in Atlantic salmon smolts fed FM-based diet or SBM-based diet with yeasts. Table S5. PERMANOVA analysis for beta-diversity of gut microbiota in Atlantic salmon smolts fed FM-based diet or SBM-based diet with yeasts. Table S6. Test of homogeneity of multivariate dispersions among dietary groups.