Additional file 1 of Modulation of Atlantic salmon (Salmo salar) gut microbiota composition and predicted metabolic capacity by feeding diets with processed black soldier fly (Hermetia illucens) larvae meals and fractions
Creators: name: Weththasinghe, Pabodha
name: Rocha, Sérgio D. C.
name: Øyås, Ove
name: Lagos, Leidy
name: Hansen, Jon Ø.
name: Mydland, Liv T.
name: Øverland, Margareth
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Rarefaction curves based on observed amplicon sequence variants (ASVs) for the different sample types. The ASV table was rarefied based on minimum sequence size (10,332) in the sample for normalization of the sequence for computation of two of the beta-diversity indices (Jaccard distance and unweighted UniFrac distance). CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S2. Principal component analysis (PCA) on standardized amplicon sequence variants (ASVs). Score plots for PC1 and PC2 (a) and PC1 and PC3 (b), mean scores (dark) with 95% confidence intervals for PC1 (c), PC2 (d), and PC3 (e), and percentage of variance explained by PCs (f). PC: principal component, CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S3. Principal component analysis (PCA) on metabolic reaction abundances (z-scores). Score plots for PC1 and PC2 (a) and PC1 and PC3 (b), mean scores (dark) with 95% confidence intervals for PC1 (c), PC2 (d), and PC3 (e), and percentage of variance explained by PCs (f). PC: principal component, CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S4. Expected and observed taxonomic profiles of the mock microbial community standard. Mock_1, Mock_2: observed taxonomic profiles of the mock. Mock_Exp: expected taxonomic profile of the mock. Figure S5. Most abundant taxa in feed samples. Top 10 most abundant taxa at phylum (comprised 100% of abundance) (a) and top 15 most abundant taxa at genus or lowest taxonomy level (comprised 61–75% of abundance) (b) in feed samples. The plots display mean abundance of each taxon within the same diet. CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S6. Linear discriminant analysis (LDA) effect size (LEfSe) results on gut microbiota of fish fed CD and DFIM diets. Circular cladogram reporting LEfSe results presents the identified amplicon sequence variants (ASVs) distributed according to phylogenetic characteristics around the circle (a). The dots closest to the center represent ASVs at the phylum level, whereas the outer circle of dots represent ASVs at the genus level. The color of the dots and sectors indicate the dietary group in which the respective ASVs are most abundant. The color explanation is given in the upper left corner. Yellow color indicates ASVs that showed similar abundance in all dietary groups. The colored sectors give information on phylum, class (full name in outermost circles, given only for phylum or class showing significant difference between groups), order, family, and genus (indicated by letter). The explanation is given below the cladogram. Indicator taxa with LDA scores of 4 or greater in the microbial communities (b). p: phylum; c: class; o: order; f: family; g: genus; CD: control diet; DFIM: defatted black soldier fly larvae meal diet. Figure S7. Linear discriminant analysis (LDA) effect size (LEfSe) results on gut microbiota of fish fed CD and DCIM diets. Circular cladogram reporting LEfSe results presents the identified amplicon sequence variants (ASVs) distributed according to phylogenetic characteristics around the circle (a). The dots closest to the center represent ASVs at the phylum level, whereas the outer circle of dots represent ASVs at the genus level. The color of the dots and sectors indicate the dietary group in which the respective ASVs are most abundant. The color explanation is given in the upper left corner. Yellow color indicates ASVs that showed similar abundance in all dietary groups. The colored sectors give information on phylum, class (full name in outermost circles, given only for phylum or class showing significant difference between groups), order, family, and genus (indicated by letter). The explanation is given below the cladogram. Indicator taxa with LDA scores of 4 or greater in the microbial communities (b). p: phylum; c: class; o: order; f: family; g: genus; CD: control diet; DCIM: de-chitinized black soldier fly larvae meal diet. Figure S8. Linear discriminant analysis (LDA) effect size (LEfSe) results on gut microbiota of fish fed CD and EX diets. Circular cladogram reporting LEfSe results presents the identified amplicon sequence variants (ASVs) distributed according to phylogenetic characteristics around the circle (a). The identified ASVs are distributed according to phylogenetic characteristics around the circle. The dots closest to the center represent ASVs at the phylum level, whereas the outer circle of dots represent ASVs at the genus level. The color of the dots and sectors indicate the dietary group in which the respective ASVs are most abundant. The color explanation is given in the upper left corner. Yellow color indicates ASVs that showed similar abundance in all dietary groups. The colored sectors give information on class (full name in outermost circles, given only for phylum or class showing significant difference between groups), order, family, and genus (indicated by letter). The explanation is given below the cladogram. Indicator taxa with LDA scores of 4 or greater in the microbial communities (b). c: class; o: order; f: family; g: genus; CD: control diet; EX: black soldier fly larvae exoskeleton diet. Figure S9. Linear discriminant analysis (LDA) effect size (LEfSe) results on gut microbiota of fish fed CD and IO diets. Circular cladogram reporting LEfSe results presents the identified amplicon sequence variants (ASVs) distributed according to phylogenetic characteristics around the circle (a). The dots closest to the center represent ASVs at the phylum level, whereas the outer circle of dots represent ASVs at the genus level. The color of the dots and sectors indicate the dietary group in which the respective ASVs are most abundant. The color explanation is given in the upper left corner. Yellow color indicates ASVs that showed similar abundance in all dietary groups. The colored sectors give information on phylum, class (full name in outermost circles, given only for phylum or class showing significant difference between groups), order, family, and genus (indicated by letter). The explanation is given below the cladogram. Indicator taxa with LDA scores of 4 or greater in the microbial communities (b). p: phylum; c: class; o: order; f: family; g: genus; CD: control diet; IO: black soldier fly larvae oil diet. Figure S10. Venn’s diagram showing the shared and unique core ASVs in digesta samples belong to insect-based groups (a), insect meal groups (b), insect lipid containing groups (c) and insect chitin containing groups (d). The core ASVs were computed using a prevalence threshold of 80%. CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S11. The beta-diversity (based on Jaccard, unweighted UniFrac, and Aitchison distance matrices) of gut microbiota in fish fed experimental diets. PCo: principal coordinate; CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S12. The boxplots for homogeneity of multivariate dispersions in gut microbiota of fish fed experimental diets. CD: control diet; IM: Full-fat BSF (black soldier fly) larvae meal diet; DFIM: Defatted BSF larvae meal diet; DCIM: De-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet. Figure S13. 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). Figure S14. Results from t-tests comparing reaction abundances between pairs 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. IO and CD (a), EX and IO (b), DCIM and CD (c), IM and CD (d), IO and DFIM (e), IO and DCIM (f), DFIM and IM (g), EX and CD (h), EX and DCIM (i), IO and IM (j), DCIM and IM (k), DFIM and CD (l), EX and DFIM (m), EX and IM (n) and DCIM and DFIM (o) groups. CD: control diet; IM: full-fat BSF (black soldier fly) larvae meal diet; DFIM: defatted BSF larvae meal diet; DCIM: de-chitinized BSF larvae meal diet; IO: BSF larvae oil diet; EX: BSF larvae exoskeleton diet.