Inhalation of ambient particulate matter (PM) can disrupt the gut microbiome, while exercise independently influences the gut microbiome by promoting beneficial bacteria. In this study, we analyzed changes in gut microbial diversity and composition in response to combined interventions of PM exposure and aerobic exercise, extending up to 12 weeks. This investigation was conducted using mice, categorized into five groups: control group (Con), exercise group (EXE), exercise group followed by 3-day exposure to PM (EXE + 3-day PM), particulate matter exposure (PM), and PM exposure with concurrent treadmill exercise (PME). Notably, the PM group exhibited markedly lower alpha diversity and richness compared to the Con group and our analysis of beta diversity revealed significant variations among the intervention groups. Members of the
Lachnospiraceae
family showed significant enhancement in the exercise intervention groups (EXE and PME) compared to the Con and PM groups. The biomarker
Lactobacillus, Coriobacteraceae
, and
Anaerofustis
were enriched in the EXE group, while
Desulfovibrionaceae
,
Mucispirillum schaedleri
,
Lactococcus
and
Anaeroplasma
were highly enriched in the PM group. Differential abundance analysis revealed that
Paraprevotella
,
Bacteroides
, and
Blautia
were less abundant in the 12-week PM exposure group than in the 3-day PM exposure group. Moreover, both the 3-day and 12-week PM exposure groups exhibited a reduced relative abundance of
Bacteroides uniformis
,
SMB53
, and
Staphylococcus
compared to non-PM exposure groups. These findings will help delineate the possible roles and associations of altered microbiota resulting from the studied interventions, paving the way for future mechanistic research.