Microbiota-tissue interaction in the skin healing of ulcered Sparus aurata after dietary administration of the probiotic SpPdp11

Figure S1. Rarefaction curves of microbiota skin samples

Figure S2. Relative abundance (%) of bacteria at the phylum in the skin mucus microbiota of fish feed with control diet without (C) and with wound (CW); fish feed with probiotic diet without (P) and with wound (PW)

Figure S3. Relative abundance (%) of bacteria at class in the skin mucus microbiota of fish feed with control diet without (C) and with wound (CW); fish feed with probiotic diet without (P) and with wound (PW). c__ non taxonomy classify OTUs at this categorise

Figure S4. Relative abundance (%) of bacteria at genera level in the skin mucus microbiota of fish feed with control diet without (C) and with wound (CW); fish feed with probiotic diet without (P) and with wound (PW).  g__ non taxonomy classify OTUs at this categorise

Figure S5.  Volcano plots of differentially expressed genes (DEGs) between groups, expression data plotted with correct p value cutoff FDR < 0.05 and log2 fold change absolute value >= 1.3. Fish feed with control diet without (C) and with wound (CW). Fish feed with probiotic diet without (P) and with wound (PW).

Figure S6. Significant functional enrichment network (A) of the "Cellular Component" and (B) "Molecular Function" GO categories (with their adjusted p) , from the DEGs obtained in the comparison of PW vs CW. Brown nodes indicates functional categories. Red to blue nodes indicate the log₂ fold change values.

Figure S7. Functional enrichment network of the KEGG terms from the DEGs obtained in the comparison of PW vs CW. The brown nodes indicate the KEGG categories, red and blue nodes show the repression overexpression and repression genes in the skin of the ulcerated probiotic group.

Figure S8. Functional enrichment network of the Reactome categories from the DEGs obtained in the comparison of PW vs CW. The brown nodes indicate the Reactome categories, red and blue nodes show the repression overexpression and repression genes in the skin of the ulcerated probiotic group. Histogram shows that the categories were significantly enriched (p adjust > 0.05)

Table S1. Results for two-way ANOVA calculation of alpha diversity indices between groups. Fish feed with control diet without (C - N) and with wound (C - W). Fish feed with probiotic diet without (P - N) and with wound (P - W). Non significance differences were showed (p > 0.05)

Table S2. DESeq2 results in P vs PW comparison at OTU level, all the taxonomy categories were showed

Table S3. RNA-seq reads summary. 1-3 biological replicate of fish feed with control diet without (C) and with wound (CW). Fish feed with probiotic diet without (P) and with wound (PW). % Respect to total reads in each case.

Table S4. Correlations of CW-PW DEGs with the genera of skin microbiota in the same tissue