Fig. 2: Characterization of recently transferred functions in the gut microbiome.

a Functions enriched in transferred genes. Plot shows fold enrichments for Pfam domains among genes transferred within species pairs relative to genes in all species. Fisher’s exact test was used to determine the significance of the annotation enrichment. Dot size and color gradient indicate -log (base 10) of the FDR values. The two-tailed p-values were corrected using the Benjamini-Hochberg FDR method. Only -Log10(FDR) \(\ge\) 8 and Log2FoldChange \(\ge\) 3 are shown. Domains highlighted in blue are functionally related to molybdenum cofactor biosynthesis. Domains highlighted in green are functionally related to mobile elements. Gene transfer network of the same segment shared between multiple genomes encoding (b) phage integrase and (c) antibiotic resistance genes. Each node represents a genome, with the corresponding taxonomy classification indicated by color. Each edge represents an HGT event observed between the genomes. The identity of the HGT event is labeled at the edge. The gene encoded in the segments is shown beside the network. d Association between species’ degree centrality in the HGT network and the presence of the MoaC gene (n = 126). Box plots show the median (center line), the 25th and 75th percentiles (box), and whiskers extending to points within 1.5 × IQR. Statistical significance was evaluated using a linear mixed-effects model to account for random effects.