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Background: Indoor microbiome exposure is associated with asthma, rhinitis and eczema. However, no studies report the interactions between environmental characteristics, indoor microbiome and health effects in a repeated cross-sectional framework. Methods: 1,279 and 1,121 preschool children in an industrial city (Taiyuan) of China were assessed for asthma, rhinitis and eczema symptoms in 2012 and 2019 by self-administered questionnaires, respectively. Bacteria and fungi in classroom vacuum dust were characterized by culture-independent amplicon sequencing. Multi-level logistic/linear regression was performed in two cross-sectional and two combined models to assess the associations. Results: The number of observed species in bacterial and fungal communities in classrooms increased significantly from 2012 to 2019, and the compositions of the microbial communities were drastically changed (p

[Display omitted] Indoor microbiome exposure is associated with asthma, rhinitis and eczema. However, no studies report the interactions between environmental characteristics, indoor microbiome and health effects in a repeated cross-sectional framework. 1,279 and 1,121 preschool children in an industrial city (Taiyuan) of China were assessed for asthma, rhinitis and eczema symptoms in 2012 and 2019 by self-administered questionnaires, respectively. Bacteria and fungi in classroom vacuum dust were characterized by culture-independent amplicon sequencing. Multi-level logistic/linear regression was performed in two cross-sectional and two combined models to assess the associations. The number of observed species in bacterial and fungal communities in classrooms increased significantly from 2012 to 2019, and the compositions of the microbial communities were drastically changed (p < 0.001). The temporal microbiome variation was significantly larger than the spatial variation within the city (p < 0.001). Annual average outdoor SO 2 concentration decreased by 60.7%, whereas NO 2 and PM 10 concentrations increased by 63.3% and 40.0% from 2012 to 2019, which were both associated with indoor microbiome variation (PERMANOVA p < 0.001). The prevalence of asthma (2.0% to 3.3%, p = 0.06) and rhinitis (28.0% to 25.3%, p = 0.13) were not significantly changed, but the prevalence of eczema was increased (3.6% to 7.0%; p < 0.001). Aspergillus subversicolor , Collinsella and Cutibacterium were positively associated with asthma, rhinitis and eczema, respectively (p < 0.01). Prevotella , Lactobacillus iners and Dolosigranulum were protectively (negatively) associated with rhinitis (p < 0.01), consistent with previous studies in the human respiratory tract. NO 2 and PM 10 concentrations were negatively associated with rhinitis in a bivariate model, but a multivariate mediation analysis revealed that Prevotella fully mediated the health effects. This is the first study to report the interactions between environmental characteristics, indoor microbiome and health in a repeated cross-sectional framework. The mediating effects of indoor microorganisms suggest incorporating biological with chemical exposure for a comprehensive exposure assessment. [ABSTRACT FROM AUTHOR]