The authors report here the development of a high-throughput, automated, inexpensive and clinically validated saliva metatranscriptome test that requires less than 100 μl of saliva. RNA is preserved at the time of sample collection, allowing for ambient-temperature transportation and storage for up to 28 days. Critically, the RNA preservative is also able to inactivate pathogenic microorganisms, rendering the samples noninfectious and allowing for safe and easy shipping. Given the unique set of convenience, low cost, safety and technical performance, this saliva metatranscriptomic test can be integrated into longitudinal, global-scale systems biology studies that will lead to an accelerated development of precision medicine, diagnostic and therapeutic tools.