Fig 1.
Identification and classification of gut microbiome MGEs.
(A) The method used to identify putative MGEs using split reads and discordantly-mapped paired-end reads. Split reads are colored blue, and discordantly-mapped paired-end reads are colored red. (B) The method used to classify MGEs based on gene signatures. (C) The number of MGE clusters identified stratified by phyla and MGE classification.
Fig 2.
Examples of niche-adaptive genes.
(A) CTn-DOT-like elements have acquired antibiotic resistance genes on multiple, independent occasions. Here, we show insertion sites of antibiotic resistant genes in CTnDOT-like elements. A CTnDOT-like ICE is shown on the left. Orthologs between elements are visualized using genoPlotR (light blue connections) and are the same color. Numbers in the top panel represent the insertion site of the numbered elements below. Antibiotic resistance genes are labeled. (B) ICEs are involved in the transfer of capsular polysaccharide biosynthesis loci between Bacteroidetes species. Here, we show examples of ICEs containing capsular polysaccharide biosynthesis loci. Orthologs between elements are plotted with GenoPlotR. Genes involved in capsular polysaccharide biosynthesis are colored orange, integrases are colored blue, and genes involved in conjugation are colored purple. Grey links indicate orthologs between elements.
Fig 3.
Tanglegram of host species lineages and phylogeny of the integrases in prophages and ICEs.
A tanglegram of tyrosine integrases from ICEs and prophages with the species lineages plotted on the left and tyrosine integrase phylogeny plotted on the right. Connections are drawn between a species and the tyrosine integrase(s) found in that species and each connecting line is colored according to host bacteria phylum.
Fig 4.
Tanglegram of host species lineages and phylogeny of serine integrases in prophages and ICEs.
A tanglegram of serine integrases from ICEs and prophages with the species lineages plotted on the left and tyrosine integrase phylogeny plotted on the right. Connections are drawn between a species and the serine integrase(s) found in that species.
Fig 5.
Examples of deletion, acquisition, and exchange of gene modules between MGEs. Orthologous genes between elements are shown with grey connections and are plotted with genoPlotR. Tyrosine integrases are colored blue, serine integrases are colored red, and genes involved in conjugation are colored purple. (A) GI73 was likely formed via a deletion of a CTnDOT-like ICE. GI90 was formed from an insertion of the ICE CTnBST into a CTnDOT-like ICE to form a large, composite GI that transfers as a unit. (B) An example of the tandem insertion of two ICEs to form a larger GI that moves as a unit. (C) An example of recombination module exchanges between ICE15 and ICE16.