Unmapped sequencing reads in livestock often contain valuable information about pathogens but are typically discarded. We analyzed blood-derived DNA and RNA from chickens and pigs kept under high- and low-biosecurity conditions, focusing on unmapped reads. In chickens, low-biosecurity farms harbored substantially more viral sequences, primarily plant viruses, indicating environmental contamination. In pigs, Mycoplasmoides pneumoniae and several pig-specific viruses were detected. Our bioinformatics pipeline, involving host read removal, assembly, BLAST, and taxonomic filtering, efficiently identified candidate pathogens and contaminants. This approach demonstrates the potential of sequencing-based environmental DNA monitoring to track microbial and viral presence, assess farm biosecurity, and support animal health surveillance.
Derks et al. (Wed,) studied this question.