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

Abstract

45Dental caries is the most common chronic infectious disease globally. The microbial communities 46 associated with caries have mainly been examined using relatively low-resolution 16S rRNA gene 47 amplicon sequencing and/or using downstream analyses that are unsound for the compositional 48 nature of the data provided by sequencing. Additionally, the relationship between caries, oral 49 microbiome composition, and host immunological markers has not been explored. In this study, 50 the oral microbiome and a panel of 38 host markers was analyzed across the saliva from 23 51 children with dentin caries and 24 children with healthy dentition. Metagenomic sequencing, 52 followed by investigation using tools designed to be robust for compositional data, illustrated 53 that several Prevotella spp. were prevalent in caries, while Rothia spp. were associated with the 54 health. The contributional diversity (extent to which multiple taxa contribute to each pathway) 55 of functional pathways present in the oral microbiome was decreased in the caries group. This 56 decrease was especially noticeable in several pathways known to impede caries pathogenesis, 57 including arginine and branched-chain amino acid biosynthesis. 10 host immunological markers 58 were found to be significantly elevated in the saliva of the caries group, and microbe-metabolite 59 co-occurrence analysis provided an atlas of relationships contributing to the bi-directional 60 influence between the oral microbiome and the host immune system. Finally, 527 metagenome-61 assembled genomes were obtained from the metagenomics data, representing 151 species. 23 62 taxa were novel genera/species and a further 20 taxa were novel species. This study thus serves 63 as a model analysis pipeline that will tremendously expand our knowledge of the oral microbiome 64 and its relationship to dental caries once applied to large populations. 65 67Dental caries is the most common chronic infectious disease and will afflict well over half of the 68 global human population at some point in their lives. Dental caries is particularly problematic in 69 children, where it is five times more common than asthma, the second most common chronic 70 disease. This extreme prevalence translates to an extraordinary economic burden. Caries 71 disproportionally afflicts vulnerable populations least able to access and afford proper treatment 72(1). Historically, members of the acid-producing and acid-tolerant mutans group of streptococci, 73 particularly the paradigm species of the group, Streptococcus mutans, were considered the 74 etiologic agents of the disease (2). While caries is certainly an infectious and transmissible 75 disease caused by the oral microbiota, it is now understood to be multifactorial and ecology-76 based, because although mutans streptococci are commonly associated with caries, they are 77 neither necessary nor sufficient to cause disease (3). Interplay between host genetic and 78 immunological factors, diet and hygiene habits, and the oral microbiota affect clinica...

Functional Profiling of Saliva Microbiome is Essential for Oral Cancer Prediction

“…Although it has long been discussed whether functional pro les outperform taxonomic pro les for microbiome classi cation tasks [76], the predicted functional pro les from OSCC-associated individuals were reported similar despite the variation of the taxonomic pro les [15]. Besides, a recent shotgun metagenomic study [77] also supports our results by discriminating healthy controls from dental caries cohorts more effectively using pathways than taxa. In contrast to our ndings, another study with gut microbiome datasets [78] showed a worse performance from function-based searches compared to those using the taxa-based strategy.…”

Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore

“…In another study of children with deep dentin caries disease, we found that bacterial community members belonging to the Rothia genus, specifically Rothia mucilaginosa, were enriched in saliva from healthy children compared to saliva from children with caries (15). From the same metagenomes, we also identified BGCs that were identical to those harbored by the complete genome sequence representing Rothia mucilaginosa ATCC 25296 (15). Based on this, we employed the oral Rothia mucilaginosa ATCC 25296 as a model species in this study.…”

“…Previously, our research team conducted a genome mining survey, targeting BGCs in 461 oral bacterial genomes, which identified a vast unexplored repertoire of ϳ5,000 putative BGCs (4). In another study of children with deep dentin caries disease, we found that bacterial community members belonging to the Rothia genus, specifically Rothia mucilaginosa, were enriched in saliva from healthy children compared to saliva from children with caries (15). From the same metagenomes, we also identified BGCs that were identical to those harbored by the complete genome sequence representing Rothia mucilaginosa ATCC 25296 (15).…”

Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle

“…Saccharibacteria (formerly TM7) have an ultrasmall cell size, reduced genomes, and are thought to be obligate epibionts, dependent on physically-associated host species (1)(2)(3). Common constituents of the oral microbiota, Saccharibacteria have been increasingly linked to inflammation and disease (4)(5)(6). Saccharibacteria contains at least 6 distinct clades (G1-G6) (7,8), however all currently available human-associated complete genomes and cultured isolates belong to clade G1, leaving clades G2-G6 quite poorly understood.…”