Objective:To explore the role of commensal microbiota in the regulation of long non-coding RNA(LncRNA)expression in mouse alveolar macrophages(AMs).Methods:AMs were separated from antibiotics-treated mice and normal mice and then were purified.LncRNA microarray technology was used to screen differentially expressed LncRNAs and conduct bioinformatics analysis.Fluorescence in situ hybridization(FISH)was used to detect the subcellular localization of LncRNA-30162.RNA interference technology was used to knock out the expression of LncRNA-30162 in RAW264.7 cells, and reverse transcription polymerase chain reation(RT-PCR) was used to detect the regulation of gene expression by LncRNA-30162 in RAW264.7 cells.Results:The purity of the separated AMs was greater than 95%.Compared with normal mice, there were 634 differentially expressed LncRNAs with changes greater than 2 folds in the AMs from antibiotics-treated mice, 363 of which were upregulated and 271 were downregulated.The target genes of differentially expressed LncRNAs were closely associated with immune system regulation, cell differentiation and chemotaxis.The expression levels of CCL24 and Arg1 in RAW264.7 macrophages were decreased after interference with LncRNA-30162 expression[(218.70±31.45) μg/L vs.(420.23±56.25) μg/L, (1.24±0.21)×10 3 U/L vs.(2.63±0.31)×10 3 U/L, t=5.416 and 6.409, P=0.006 and 0.003]. Conclusions:Commensal microbiota can regulate the expression of LncRNAs in AMs.Differentially expressed LncRNAs are associated with a variety of gene ontology(GO)biological processes and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways.LncRNA-30162 can regulate the expression levels of CCL24 and ARG1 in RAW264.7 cells.