The microbiota present in the respiratory tract (RT) responds to environmental stimuli and engages in a continuous interaction with the host immune system to maintain homeostasis. A total of 40 C57BL/6 mice were divided into four groups and exposed to varying concentrations of PM nitrate aerosol and clean air. After 10 weeks of exposure, assessments were conducted on the lung and airway microbiome, lung functions, and pulmonary inflammation. Additionally, we analyzed data from both mouse and human respiratory tract (RT) microbiomes to identify possible biomarkers for PM exposure-induced pulmonary damages. On average, 1.5 and 13.5% inter-individual microbiome variations in the lung and airway were explained by exposure, respectively. In the airway, among the 60 bacterial OTUs (operational taxonomic units) > 0.05% proportion, 40 OTUs were significantly affected by PM exposure (FDR ≤ 10%). Further, the airway microbiome was associated with peak expiratory flow (PEF) ( = 0.003), pulmonary neutrophil counts ( = 0.01), and alveolar 8-OHdG oxidative lesions ( = 0.0078). The order bacteria showed the strongest signals. For example, the OTU was elevated by PM nitrate exposure ( = 4.98 × 10) and negatively correlated with PEF ( = -0.585 and = 2.4 × 10). It was also associated with the higher pulmonary neutrophil count ( = 8.47 × 10) and oxidative lesion ( = 7.17 × 10). In human data, we confirmed the association of airway order bacteria with PM exposure and lung function. For the first time, this study characterizes the impact of PM exposure on the microbiome of multiple sites in the respiratory tract (RT) and its relevance to airflow obstructive diseases. By analyzing data from both humans and mice, we have identified bacteria belonging to the order as a promising biomarker for PM exposure-induced decline in pulmonary function and inflammation.