Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance

Mobile genetic elements (MGEs) are key promoters of bacterial and archaeal genome evolution. These elements can be located extrachromosomally (such as plasmids) or integrated within the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are the integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies so far have focused on the biological mechanisms that shape the lifestyle of these elements. It is crucial to illustrate the overall diversity and understand the distribution of circulating ciMGEs in the microbial community as the number of genome sequences increases exponentially. Herein, I scanned a publicly available collection of more than 20000 bacterial and archaeal non-redundant genomes and found more than 13000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs currently available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defensive systems, virulence genes, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, I discovered that defense systems, AMR, and virulence genes are negatively correlated in both ICEs and IMEs. Multiple representatives of these ciMGEs form heterogeneous communities and challenge interphylum barriers. Finally, I observed that the functional landscape of ICEs is populated by uncharacterized proteins. Taken together, this study provides a comprehensive catalog compiling the nucleotide sequence and associated metadata for ciMGEs from 34 distinct phyla across the bacterial and archaeal domains.