Paper

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

Banavar, Guruduth, Molusky, Matthew M, Julian, Cristina, Vuyisich, Momchilo, Gorakshakar, Anmol, Hu, Lan, Oyetunji Ogundijo, Patridge, Eric, Janevski, Angel

2023

Overview

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.Competing Interest StatementThe material represents original research, has not been previously published (is deposited as a preprint in biorxiv.org) and has not been submitted for publication elsewhere while under consideration in CSBJ. All authors of this manuscript were employees of Viome Life Sciences Inc at the time of their contributions, and held stock options in the company. MV and GB hold management positions within the company. The work was funded by Viome Life Sciences Inc.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Addictions / Life sciences / Oral cavity / Periodontal diseases / Phenotypes / Saliva / Systems Biology