Altogether, the crosstalk between the gut microbiome and the lungs through the ‘gut–lung axis’ is complex and may involve multiple mechanisms, including immune response, metabolic disorders, cytokines, inflammation, etc. However, in the present study, we found that gut microbiome dysbiosis induced by clindamycin disturbs the gut equilibrium between bacteria and fungi, alters the lung transcriptome, and increases Nos2 expression. This evidence concerns the gene NOS2 and Other metabolic disease.