Table 1 Microbe types for mNGS data interpretation
Microbe type | Bioinformatic parameter | Positive threshold | Borderline positive threshold | Examples |
|---|---|---|---|---|
Commensal | RAR |  > 30% or fourfold greater than any other microbes | 15–30% or 2–fourfold greater than any other microbes | Prevotella, Veillonella, and Candida |
Putative pathogen | RAR |  > 10% | 5–10% | Acinetobacter baumannii, Enterobacteriaceae, Enterococcus, Staphylococcus |
Absolute pathogen | MRN |  > 1 either the species or genus level | / | Mycobacterium tuberculosis (MTB), Cryptococcus, and Pneumocystis japonicum (PJP) |
Virus | MRN |  > 6 | / | / |
NTM* | RAR | top 10 in the bacterial genus level | / | / |