Abstract <p>Exposure to cadmium (Cd), a toxic heavy metal, is a severe threat to organismal health, causing a wide range of pathological alterations in various tissues and organs. Alterations in the composition and function of the gut microbiome have been indicated across numerous animals exposed to Cd. However, the impact of Cd inhalation exposure on the pulmonary microbiome has not been well investigated yet. Therefore, in this study, we investigated the effects of exposure to CdONPs and its clearance on both colonic and pulmonary microbiomes in mice. The diversity of both colonic and pulmonary microbiomes of exposed mice was significantly affected after 9&#xa0;weeks of CdONPs inhalation. The effects of CdONPs exposure on bacterial composition and function were more pronounced in the colonic microbiome than in the pulmonary microbiome. The clearance was more efficient in the restoration of gut microbiome composition in comparison to the lung microbiome. Moreover, we evaluated a bidirectional interaction between Cd exposure and gut microbiota. <i>Duncaniella</i>, <i>Odoribacter</i>, and <i>Pontibacter</i> were the prominent biomarkers that significantly positively correlated with dysregulated functions in the colonic microbiome of exposed mice. Based on the PICRUSt2 prediction analysis, our results suggested that perturbations in the gut microbiota balance due to Cd exposure were associated with the increase in the proportion level of bacteria with excessive membrane transporters, which may potentially augment the absorption of this metal by intestinal microbiota thereby leading to the accumulation of Cd in intestinal bacteria and the potential alleviation of the Cd toxicity effect. Furthermore, genes related to metal chelators were consistent with the colonic microbiome of exposed mice, suggesting possible promotion of Cd excretion and its eventual fecal elimination. However, these observations derived from 16S rRNA profiling and PICRUSt2 predictions would need to be verified experimentally to establish any functional or mechanistic implications. This could be considered a key factor in determining the intestinal bacterial species able to minimize the toxicity of heavy metals in future therapeutic approaches.</p> Key points <p>• <i>Inhalation of CdO nanoparticles significantly alters both gut and pulmonary microbiome composition and diversity in mice.</i></p> <p>• <i>Microbiome changes are more pronounced in the gut than in the lungs following inhalation exposure.</i></p> <p>• <i>Partial recovery of microbiome composition occurs after the clearance period, with greater restoration in the gut than in the lung.</i></p> <p>• <i>Predicted functional profiles indicate shifts in microbial metabolic potential associated with Cd exposure.</i></p> <p>• <i>The findings support a potential interaction between inhaled Cd exposure and the gut microbiome, highlighting the relevance of the gut–lung axis.</i></p> Graphical Abstract <p></p>