Methods and systems for detecting unwanted microbes, and the origins thereof, in an environment are disclosed herein. The methods disclosed herein can be applied to a wide range of environments, including, but not limited to, food production facilities, office facilities, and public facilities. The methods comprise obtaining one or more samples from one or more locations in an environment, sequencing a plurality of
nucleic acid sequences within the samples, identifying one or more indicator microbial signatures or origin-indicating microbial signatures within the plurality of
nucleic acid sequences, comparing the indicator microbial signatures against one or more databases, and identifying one or more unwanted microbes, and / or the origins thereof, that correspond to one or more of the microbial signatures identified.