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

Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host immunological markers were analyzed across 23 children with caries and 24 children with healthy dentition. Ten host markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential microbe-marker relationships. Furthermore, 527 metagenome-assembled genomes (MAGs) were obtained, representing 150 bacterial species. 42 of these species had no genomes in public repositories, representing novel taxa. This data greatly expanded the pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other Saccharibacteria. This study illustrated the oral microbiome at an unprecedented resolution, and provided several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.