In the PB3P project, we isolated 100 bacterial colonies associated with Fusobacterium nucleatum, a key player in the development of peri-implant diseases. We managed to identify clear microbial signatures of healthy, mucositis and peri-implantitis implants, with the latest mainly composed of PiRC™ species and new uncharacterized ones. Using the reconstructed and isolated genomes, we further expanded the F. nucleatum phylogenetic tree composed of 5 different subspecies of which we characterized the antibiotic profiles and the presence of virulence factors.