Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children

Abstract

Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

“…have been associated with both health and dental caries, depending on the study. Our findings are in line with several studies that associated Prevotella with dental caries (21, 59–61), including one that found it was the best predictor of childhood caries (59). These reports were in contrast to a study where Prevotella were enriched in the healthy cohort (62).…”

“…This indicates that S. mutans, when present, has a large influence on the pathogenicity of the oral microbiome due to its prodigious capacity to generate insoluble glucans and resultant biofilms (9, 26). Other oral microbiome studies have found S. mutans at low abundances (20, 21, 54), and the use of saliva in this study may explain its rarity, and possibly underestimation, here—as an exceptional biofilm-former, it is less likely to be shed from its dental plaque residence into the salivary milieu (55).…”

Supragingival mycobiome and inter-kingdom interactions in dental caries

“…We have recently used whole metagenome sequencing (WMS) to study the supragingival microbiome in 30 children with various levels of carious severity [9]. In WMS, all fragments of DNA in a sample are sequenced, which allows exploring the different categories of microorganisms present in the sample.…”

Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research

“…The DNA isolation method, hereafter referred to as the "MetaSUB method", was developed for the MetaSUB Consortium (www.metasub.org) to complement an ongoing global effort to characterize subway and urban environment microbiomes using surface swab samples, by extending the effort to also include air samples. The MetaSUB method was benchmarked against two other state-ofthe-art DNA isolation methods: a custom multicomponent DNA isolation method developed for use in aerosol microbiome research published by Jiang et al [28], and the commercial ZymoBIOMICS DNA Microprep Kit commonly used in environmental microbiome studies [38][39][40][41]. The performance of the three DNA isolation methods was evaluated using both a mock microbial community and real-world low biomass subway air samples.…”