{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T17:28:34Z","timestamp":1786123714052,"version":"build-2736575974"},"posted":{"date-parts":[[2026,8,5]]},"group-title":"Microbiology","reference-count":112,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"NIH","award":["R01DE016937"],"award-info":[{"award-number":["R01DE016937"]}]},{"name":"NIH","award":["T32DE023526"],"award-info":[{"award-number":["T32DE023526"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,8,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Porphyromonas gingivalis<\/jats:italic>\n                    (\n                    <jats:italic>Pg<\/jats:italic>\n                    ) is an oral pathobiont that contributes to periodontal disease and has been associated with systemic health conditions. Although\n                    <jats:italic>Pg<\/jats:italic>\n                    is recognized as exhibiting extensive strain-level genomic diversity and recombination, the extent to which mobile elements contribute to this variation, and their relevance to its fitness and virulence, remain incompletely understood. Our recent study of the\n                    <jats:italic>Pg<\/jats:italic>\n                    pangenome revealed diverse accessory defense-associated genes, raising the question of whether these are carried by unrecognized mobile genetic elements (MGEs). Integrative and conjugative elements (ICEs) are large autonomous mobile elements that often encode genes for proteins beneficial to their bacterial hosts, including defense systems that protect against phage infection. To date, only one ICE, CTnPg1, has been described in\n                    <jats:italic>Pg<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    Here, we developed a bioinformatic approach integrating ICE prediction and curation, hallmark-gene detection, and genomic-context analysis, to investigate ICEs in\n                    <jats:italic>Pg<\/jats:italic>\n                    . We discovered that ICEs are pervasive in\n                    <jats:italic>Pg<\/jats:italic>\n                    genomes, with &gt;90% of genomes harboring at least one ICE. We found that these elements comprise at least five distinct groups, two of which dominate and frequently co-occur in\n                    <jats:italic>Pg<\/jats:italic>\n                    genomes, inserting into distinct characteristic insertion sites. Using marker-gene analysis of enrichment-culture mini-metagenomes from subjects with periodontal disease we detected representatives of these dominant\n                    <jats:italic>Pg<\/jats:italic>\n                    ICE groups, as well as others, in recent clinical samples. We found that anti-defense and defense genes are common in\n                    <jats:italic>Pg<\/jats:italic>\n                    ICEs, and that these elements commonly encode biosynthetic gene clusters, including for menaquinone synthesis and predicted ribosomally synthesized and post-translationally modified peptides (RiPPs). In contrast to the extensive CRISPR-Cas defense targeting we observed for\n                    <jats:italic>Pg<\/jats:italic>\n                    phages, we detected no exact matches between ICE sequences and\n                    <jats:italic>Pg<\/jats:italic>\n                    CRISPR spacers.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>\n                    This work establishes that ICEs are pervasive contributors to\n                    <jats:italic>Pg<\/jats:italic>\n                    \u2019s pangenome and unique strain-level gene repertoires. Their distinct cargo profiles suggest that ICEs likely impact the virulence and ecology of\n                    <jats:italic>Pg<\/jats:italic>\n                    through the introduction and spread of advantageous traits, including expansion of\n                    <jats:italic>Pg<\/jats:italic>\n                    \u2019s biosynthetic capacity and resistance to phage infection. This work provides a curated framework for investigating ICE diversity in\n                    <jats:italic>Pg<\/jats:italic>\n                    and establishes a foundation for expanded experimental studies of their host ranges and roles in shaping\n                    <jats:italic>Pg<\/jats:italic>\n                    \u2019s interactions with phages, other microbes, and the human host.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.08.04.741601","type":"posted-content","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T06:25:16Z","timestamp":1785997516000},"source":"Crossref","is-referenced-by-count":0,"title":["Pervasive integrative and conjugative elements shape\n                  <i>Porphyromonas gingivalis<\/i>\n                  gene repertoires"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7559-8460","authenticated-orcid":false,"given":"Cole 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