Fig. 4
Distribution of the core OTUs and the goodness-of-fit to neutral model for the gut microbiota. The OTUs presented in > 70% samples were defined as core taxa. Core taxa were determined in each of four batches (A) and all individuals from each source (B). The boxplot shows the relative abundance (left axis) and diamonds are represented detected frequency (right axis) in farmed and wild samples (B). The goodness-of-fit to the neutral model for the farmed (C) and wild samples (D). The dashed curve (in C and D) represents 99% confidence intervals of the model prediction. R2 indicates the goodness-of-fit to the neutral model. Pie charts show the proportion of within, above, and below the prediction of high-abundance OTUs (relative abundance > 10−3 as separated by the vertical dash line). E Violin plot of nearest taxon index (NTI) and beta nearest taxon index (βNTI). Horizontal dashed lines (NTI or βNTI values at − 2 and 2) indicate thresholds for determining the assembly pattern [66].