Geographic Variation and Core Signatures of the Root Canal Microbiome: A Cross-Country Comparative Study

Root canal infections harbour complex microbial communities that may vary across geographic populations. This study aimed to compare the root canal microbiome across Spain, Sweden, and the USA, identifying key microbial taxa, compositional and functional differences, and cohort-associated microbial signatures.

16S rRNA gene sequencing datasets from primary root canal infections were retrieved from three geographic cohorts (Spain n = 32, Sweden n = 14, USA n = 25). All samples targeted the V3-V4 region and were sequenced using the Illumina MiSeq platform. Alpha and beta diversity metrics were assessed to evaluate within- and between-sample variation. Taxonomic composition was characterized, followed by differential abundance analysis and identification of the core microbiome. Microbial co-occurrence networks were inferred using the SPRING method, and hub taxa were identified based on eigenvector centrality.

Significant differences in microbial richness between cohorts were observed based on Chao1 index and observed richness. Beta diversity analyses revealed statistically significant but modest separation of microbial communities among populations (R² = 6.8%), with substantial overlap between cohorts. Bacillota, Bacteroidota, Fusobacteriota, and Actinomycetota were dominant across cohorts, although their relative abundances varied. Core microbiome analysis identified both shared and cohort-associated taxa at genus and species levels. SPRING-based co-occurrence networks identified cohort-associated hub taxa, including Fretibacterium fastidiosum in the USA, Dialister pneumosintes in Spain, and Treponema denticola in Sweden. Furthermore, predictive functional profiling suggested differences in microbial functional potential among geographic cohorts.

While root canal infections share a core microbiome, subtle population-specific microbial signatures were identified. However, the modest effect size suggests that geographic variation alone explains only a limited proportion of microbial composition. Larger and more balanced studies are required to further evaluate geographic influences on the root canal microbiome and their potential clinical relevance.