Matrishin, C. B. | bioRxiv Science

bioRxiv2026

Pervasive integrative and conjugative elements shape Porphyromonas gingivalis gene repertoires

BackgroundPorphyromonas gingivalis (Pg) is an oral pathobiont that contributes to periodontal disease and has been associated with systemic health conditions. Although Pg 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 Pg 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 Pg. ResultsHere, we developed a bioinformatic approach integrating ICE prediction and curation, hallmark-gene detection, and genomic-context analysis, to investigate ICEs in Pg. We discovered that ICEs are pervasive in Pg genomes, with >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 Pg 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 Pg ICE groups, as well as others, in recent clinical samples. We found that anti-defense and defense genes are common in Pg 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 Pg phages, we detected no exact matches between ICE sequences and Pg CRISPR spacers. ConclusionThis work establishes that ICEs are pervasive contributors to Pgs pangenome and unique strain-level gene repertoires. Their distinct cargo profiles suggest that ICEs likely impact the virulence and ecology of Pg through the introduction and spread of advantageous traits, including expansion of Pgs biosynthetic capacity and resistance to phage infection. This work provides a curated framework for investigating ICE diversity in Pg and establishes a foundation for expanded experimental studies of their host ranges and roles in shaping Pgs interactions with phages, other microbes, and the human host.

microbiology↗

bioRxiv2022

Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

BackgroundPorphyromonas gingivalis (hereafter "Pg") is an oral pathogen that can act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. A key force shaping strain level diversity in all microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg. ResultsHere we systematically addressed the question of whether Pg are infected by phages - and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures. DiscussionThis work definitively establishes that phages are a major unrecognized force shaping the ecology and intraspecies strain-level diversity of the well-studied oral pathogen Pg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.

microbiology↗