Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics
Paolo Ghensi, Paolo Manghi, Moreno Zolfo, Federica Armanini, Edoardo Pasolli, Mattia Bolzan, Alberto Bertelle, Federico Dell’Acqua, Ester Dellasega, Romina Waldner, Francesco Tessarolo, Cristiano Tomasi, Nicola Segata
Abstract
Dental implants are installed in an increasing number of patients. Mucositis and peri-implantitis are common microbial-biofilm-associated diseases affecting the tissues that surround the dental implant and are a major medical and socioeconomic burden. By metagenomic sequencing of the plaque microbiome in different peri-implant health and disease conditions (113 samples from 72 individuals), we found microbial signatures for peri-implantitis and mucositis and defined the peri-implantitis-related complex (PiRC) composed by the 7 most discriminative bacteria. The peri-implantitis microbiome is site specific as contralateral healthy sites resembled more the microbiome of healthy implants, while mucositis was specifically enriched for Fusobacterium nucleatum acting as a keystone colonizer. Microbiome-based machine learning showed high diagnostic and prognostic power for peri-implant diseases and strain-level profiling identified a previously uncharacterized subspecies of F. nucleatum to be particularly associated with disease. Altogether, we associated the plaque microbiome with peri-implant diseases and identified microbial signatures of disease severity.