Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing.

Background: The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology.

Objectives: To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses.

Materials and methods: Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups. All prosthesis plaque samples underwent 2bRAD metagenomic sequencing to characterize the species-resolved microbial composition. MIPs for clean and unclean prostheses were calculated based on the sum of the relative abundance of pathogenic bacteria in a microbiome using a reference database that contains opportunistic pathogenic bacteria and disease-associated information.

Results: Beta diversity analyses based on Jaccard qualitative and Bray-Curtis quantitative distance matrices identified significant differences between the two groups (p < 0.05). There was a significant enrichment of many pathogenic bacteria in the unclean prosthesis group. The MIP for unclean prostheses (0.47 ± 0.25) was significantly higher than for clean prostheses (0.37 ± 0.29), p = 0.029.

Conclusions: The microbial community of plaque samples from 'unclean' prostheses demonstrated compositional differences compared with 'clean' prostheses. In addition, the pathogenic microbiome in the 'unclean' versus 'clean' group differed.