Provided herein are, inter alia, methods, compositions, and systems, for detecting and treating lung dysbiosis. In aspects, included herein are methods, compositions, and systems for detecting infections (such as Aspergillus sp. infections and Mycobacterium sp. infections), or the risk thereof, as well as for treating such infections. Also provided are methods, compositions, and systems for detecting whether a subject who has pneumonia and is infected with HI has an increased risk of dying compared to a general population of subjects who have pneumonia and are infected with HIV. Methods, compositions, and systems for monitoring subjects diagnosted as having a disease or risk as disclosed herein are also included.
