Metagenomic shotgun sequencing of Exhaust Air Dust

Metagenomic next-generation sequencing analysis was performed on nucleic acids isolated from EAD filters collecting air from: (1) cages with mice housed in a non-pathogen free facility; (2) cages with clean chow and bedding from the same facility; (3) cages housing mice from a specific-pathogen free (SPF) facility. mNGS results revealed correspondence between microbiome composition from fecal pellets and filter, including pathogenic bacteria, intestinal protozoa, nematoda and eukaryotic parasites present in the colony. All filters revealed also the presence of plant microbiome due to dust derived from chow and bedding. Surprisingly, however, control filter exhibited the presence of mouse pathogens, despite the absence of mice, suggesting that contaminated connecting pipes could be responsible for this unexpected result. Conversely, the filter from SPF colony revealed the absence of pathogens.