Fig. 3: Species involved in HGT tend to have stronger co-abundance correlation.

a Distribution of various types of correlation among species pairs. Each two-letter code represents the correlation observed at baseline and follow-up (N for negative, P for positive, U for uncorrelated). Correlations that are stable over time (N-N and P-P) are highlighted in the red box. b Plots showing the change in correlation in species pairs at baseline and follow-up. Temporal changes in species pairs’ correlation with no HGT are shown at left and in those with HGT at right. c Microbial Co-Abundance Network. In this network, edge lengths reflect the strength of species correlations, with shorter edges indicating stronger associations. Nodes are color-coded based on Leiden clustering, and edges are colored according to the type of relationship (blue for negative correlations, red for positive correlations, green for HGT transfers). d The three largest sub-communities identified are Community A (n = 47), Community B (n = 44), and Community C (n = 92). Upper panel shows the co-abundance relationship, where edge colors indicate positive correlations in red and negative correlations in blue. The lower panel shows the HGT relationships, with green edges representing HGT events. e Temporal Stability of Sub-Communities. The y-axis represents the Bray-Curtis distance of species abundance within each sub-community between baseline and follow-up (n = 338). Box plots show the median (center line), the 25th and 75th percentiles (box), and whiskers extending to points within 1.5×IQR. The LMM with phylogenetic distance matrices was fitted to examine the association. f Association between HGT rates and phylogenetic distance of species pairs (n = 237). Bars show the average HGT rates across all species pairs in each bin. The association was evaluated using a linear regression model. g Association between co-abundance and phylogenetic distance of species pairs (n = 3896). Bars show the average correlation value across all species pairs in each bin. The association was evaluated using a linear regression model (see Methods). h Association between HGT occurrence and co-abundance of species pairs (n = 237). The half violin presents the co-abundance distribution when HGT occurred (blue) and did not occur (green) between species pairs. The association between co-abundance and HGT occurrence (0/1) while adjusting for phylogenetic distance was assessed using a partial Mantel test with 9999 permutations. Boxplots show median (center line), IQR (box), and 1.5 × IQR whiskers. p-values were FDR-corrected.