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. 2024 Feb 22;16(1):2317059.
doi: 10.1080/20002297.2024.2317059. eCollection 2024.

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

Tong Wah Lim  1 , Shi Huang  2 , Yuesong Jiang  2 , Yufeng Zhang  2 , Michael Francis Burrow  1 , Colman McGrath  2
Affiliations

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

Tong Wah Lim et al. J Oral Microbiol. .

Abstract

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.

Keywords: Removable prosthesis; metagenomics; microbial index; pathogenic bacteria; prosthesis cleanliness.

Plain language summary

The pathogenic microbiome in the unclean removable prosthesis group tends to be more abundant than that of the clean counterpart among participants with the majority being elders attending a teaching hospital. This finding is worrying because a general decline in systemic health among community-dwelling elders may predispose them to life-threatening diseases.By understanding the characteristics of the microbiome of removable prostheses with different levels of cleanliness and the related microbial-infection risks after a comprehensive whole metagenomic sequencing, appropriate prosthesis hygiene care should be emphasized.This study introduced a comprehensive and novel method of microbiological investigation of plaque using 2bRAD-M. The taxonomic profile of the microbiome of whole genomes was demonstrated and resolved at the species-level taxonomy for prosthesis biofilms. The biggest advantage of this method included overcoming the DNA sample problems particularly the low-biomass nature of ‘clean’ prosthesis plaque samples. The findings will add to our understanding of the microbiological aspect of removable prosthesis plaque.

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Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Shannon diversity with the number of samples sequenced revealed adequate sample size for species detection.
Figure 2.
Figure 2.
a) alpha diversity analysis (Chao 1) revealed no significant difference in microbial richness between clean and unclean prostheses (p = 0.066). b) beta diversity analysis, Principal Coordinate analysis based on the Jaccard (PERMANOVA; R2 = 0.026, p = 0.001) distance matrix.
Figure 3.
Figure 3.
Boxplot of the ratios between the relative abundance of human and bacterial DNA.
Figure 4.
Figure 4.
Top 30 most abundant species in the removable prosthesis biofilm.
Figure 5.
Figure 5.
The LEfSe analysis indicated a higher abundance of 48 taxa in the unclean prosthesis group than in clean prostheses. The brightness of each point was proportional to the size of its effect.
See this image and copyright information in PMC

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