Metatranscriptomics of the human oral microbiome during health and disease

The human microbiome plays important roles in health, but when disrupted these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite inter-patient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that healthy and diseased communities exhibit defined differences in metabolism that are conserved between patients. In contrast, individual species metabolic gene expression was highly variable between patients. These results demonstrate that despite high inter-patient variability in microbial composition, diseased communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes.