Fig. 4

Ct values comparison across groups of samples. The boxplot shows the qPCR Ct values for all sample groups. Groups of samples before formalin treatment are on the left side of the plot, while those after treatment are on the right. Gut content samples are colored in blue while gut mucosa samples in red. Color intensity discriminates between healthy (light) and sick (darker). ANOVA coupled with a Tukey’s HSD post-hoc test for pairwise comparisons was performed. Differences in the mean Ct values across groups can be seen when comparing groups of healthy fish with their sick counterpart (e.g. CHB vs CSB) and when distal gut content groups with their distal gut mucosa counterpart (e.g. CHB vs MHB). Sick fish present lower Ct values than the healthy ones indicating an increase in the total microbial biomass in relation to disease progression, and gut mucosa samples harbor a lower total microbial biomass than the gut content. No difference in the Ct values could be detected in response to formalin treatment indicating a negligible direct effect on the gut total microbial content. Statistically significant differences in the mean Ct value between groups are highlighted for biologically relevant comparisons (see Additional file 9 for all the comparisons p-values)