Table 1.
Descriptive statistics of sequencing to determine the microbiotoa for each individual.
Figure 1.
Taxonomic structure of the bacterial community of fish skin mucus at three different taxonomic levels: Phylum, Classl and OTU.
a) Proteobacteria; b) Bacteroidetes, c) Alphaproteobacteria, d) Flavobacteria, e) Gammaproteobacteria, f) OTU 50 (Methylobacterium rhodesianum), g) OTU 36 (Flavobacterium psychrophilum).
Table 2.
Taxonomic variation observed between male and female.
Figure 2.
Dendrogram analysis based upon ThetaYC index of bacteria found on the skin of the 86 brook charr individuals.
Groups are defined with the Weighted Unifrac distance. The first and second groups are composed of closely related bacterial communities. The third group is an assemblage of dissimilar communities and is considered as an outgroup. The most differentiated groups are groups 1 and 3 (Unifrac Score: 0.710811, p<0.0010) followed by the distance between groups 2 and 3 (Unifrac Score: 0.685361, p<0.0010), and the distance between groups 1 and 2 (Unifrac Score: 0.401674, p<0.0010).
Figure 3.
Alpha diversity of each group.
Each group was defined by the dendrogram analysis based upon ThetaYC index (see figure 2). Alpha-diversity was calculated by the non-parametric index of Shannon.
Figure 4.
Descriptive analysis of the Metastats.
Numbers indicates the numbers of OTUs differentially present in the different groups of individuals. For details on the identities of the OTUs, please refer to the table 3; 4 and 5.
Table 3.
Detailed information related to the OTU differentially abundant between individuals belonging to group 1 and group 2.
Table 4.
Detailed information related to the OTU differentially abundant between individuals belonging to group 1 and group 3.
Table 5.
Detailed information related to the OTU differentially abundant between individuals belonging to group 2 and group 3.
Figure 5.
PCoA analysis of the microbiome for all 86 F2 individuals based on the Yue & Clayton measure of dissimilarity (Thetayc).
Black circles represent individuals belonging to the group 1, red circles represent individuals belonging to the group 2 and green circles represent individuals belonging to the group 3. Arrows represent genus, which are significantly correlated with the axis. The first and second axes represented 24.5% and 7.7% of the variation respectively. The R-squared between the original distance matrix and the distance between the points in 2D PCoA space was 0.87.
Figure 6.
Relationship between the Fulton Index and and the abundance of the OTU 36.
A linear regression is observed based on a linear model (Shapiro test for Normality: p-value = 0.07, Linear model: p-value = 0.02741, F = 5.0388, Rsq = 0.04536).
Table 6.
Descriptive statistics, including the LOD score, the position, 95% CI, PVE (%), the associated P-value of each QTL linked to every phenotype related to bacteria counts trait (LOD, Log10 of the odd ratio; 95% CI, 95% confidence interval; PVE, percent variance explained) [23].