Metagenomic and Metatranscriptomic Examinations of the Oral Microbiome in Health and Disease

Dental caries is one of most common chronic health conditions, affecting nearly 3.5 billion people worldwide to an estimated economic cost of $245 billion. The role of host genetics in structuring the oral microbiome is not clear.   While it is unequivocal that the oral microbiome is responsible for the formation of caries, there are conflicting views about whether it is a single taxa or ecological disease. The diagnosis of caries currently involves direct observation by a professional, indicating a possible need for leading molecular diagnostics. Using 16S, metagenomic, and metatranscriptome surveys of oral plaque sampled from a twins cohort, we addressed each of these issues.  We found that the oral microbiota does include heritable taxa and that the oral microbiome was always more similar in a shared host genotype. An iterative subject-specific metagenomic assembly pipeline generated 658 bacterial, 179 DNA virus, and 10 RNA virus metagenome assembled genomes. Grouping into species level clusters revealed that the Gracillibacteria are highly personalized, while many other taxa such as Cardiobacter are conserved genomically across the entire sample population, which has implications for the development of oral microbiome based forensic approaches. We applied novel feature engineering and compositionally-aware ensemble network frameworks to the integrated metagenomic and metatranscriptomic data. These methods can be applied when hypothesis testing for differential abundance do not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a co-expression network but also how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core oral microbiome composed of both bacteria and viruses that were transcriptionally active in all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.