Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness

Abstract

It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n=9,350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n=14,129). As clinical validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions.HighlightsMicrobial functional pathways in the oral cavity are quantified as eight oral scoresScores are significantly worse for individuals with oropharyngeal disease phenotypesThis methodology may be generalized to other pathways and other sample typesThese scores provide longitudinal health insights in a precision wellness applicationGraphical Abstract

Altered gut microbial functional pathways in people with Irritable Bowel Syndrome enable precision health insights

“…As we previously published [43], our Score Development Framework is a 5-step process. A high level summary for each of the eight gut pathway scores appears in Table 6, including key functions and a brief description of microbial activities.…”