Fig. 4: Mobilome and the ultraconserved plasmids in the LRT microbiome.

a Bar plot showing the prevalence of the top six most abundant mobile genetic elements (MGEs) identified in the LRT microbiome (n = 105). The plot includes vertical bars representing the mean values. Whiskers extend upward from the top of each bar, with the upper end of the whisker representing the mean plus one standard error (SD). b Panels indicating the average number of each type of MGEs for each species identified in our MAGs (n = 105). EHMOS represents a group of less prevalent opportunistic pathogens, including Elizabethkingia anophelis (E), Haemophilus influenzae (H), Prevotella melaninogenica (M), Prevotella oris (O), and Neisseria subflava (S). The plot includes a center line (median), box limits (upper and lower quartiles), and whiskers (1.5x interquartile range). Individual data points are shown using overlaid dot plots. Significance was determined using the two-sided Wilcoxon rank sum test. The exact p-values are directly annotated on the plot. c An analysis of the length distribution of the identified MGEs in each species. The x-axis indicates the length of MGEs, and the y-axis indicates the count. Significance was determined using the two-sided Kolmogorov-Smirnov test. The exact p-values are annotated on the plot for significant comparisons. d Sankey diagram showing the distribution of different types of MGEs (middle) identified in the five predominant species (left) linking to the antibiotic resistance genes (ARGs; right). e The schematic map for the representative plasmid identified in our samples. The gene names are labeled based on the annotation using eggNOG. f Pairwise average nucleotide identity (ANI) analysis of a highly conserved plasmid in Acinetobacter baumannii. Additional metadata, including the NCBI RefSeq ID, sampling site, and collection time of each plasmid sequence, are annotated on the plot. g The alignment map showing the whole-genome comparisons for two Acinetobacter baumannii plasmids discovered in 1982 and 2021 (the latter identified in our samples), respectively. The e-value for the two major regions was calculated using Blast. Source data are provided as a Source Data file. Abbreviation: IS, insertion sequences; MITE, miniature inverted repeats; ICE, integrative conjugative elements; ANI, average nucleotide identity.