This repository contains custom computer codes for main analyses in manuscript 'Skin commensal bacteria regulate lung microbiota to alleviate allergic asthma'.

When the ancestors of humans ventured onto land hundreds of millions of years ago, exposure to air simultaneously altered the host's lung and skin microbiota. Evolution shaped the cross-organ tolerance of host immune system to commensals, which in turn regulate excessive immune responses in the host. Through multi-center cohort studies and mouse models, we demonstrated that in atopic dermatitis, skin commensal Staphylococcus epidermidis (S. epidermidis) produces indole-3-lactic acid (ILA) to activate aryl hydrocarbon receptor (AhR) in the lung via systemic circulation. This activation dependently increases lung commensal Rothia mucilaginosa (R. mucilaginosa) abundance, elevating short-chain fatty acids (SCFAs) concentration in the lung environment to alleviate atopic march (the progression from atopic dermatitis to allergic asthma). These findings identify a conserved cross-organ microbial adaptive evolution strategy against excessive host immunity, offering clues for therapies targeting inter-organ bacterial crosstalk in immune regulation.

• code/seurat_utils.R + code/cellchat_utils.R: streamlined Seurat and CellChat workflows.
• code/microbiome_utils.R + code/microbiome_prediction_utils.R: microbiome stats, ordination, and prediction helpers.
• code/enrichment_utils.R + code/kegg_utils.R + code/limma_utils.R: differential testing and KEGG/GSEA enrichment.
• code/metabolism_utils.R + code/heatmap_utils.R + code/plot_utils.R + code/theme_utils.R: metabolite cleanup plus ready-made plots, heatmaps, and themes.
• code/multiomics_utils.R + code/lefse_utils.R + code/iobr_utils.R + code/tempdir_utils.R: multi-omics merging, LEfSe wrappers, signature scoring, and fixed temp directories.

• Single-cell RNA-seq transcriptomics: GEO GSE310069.
• 16S rRNA gene sequences: NCBI PRJNA1345678.

Skin commensal bacteria regulate lung microbiota to alleviate allergic asthma; Under Review, 2026

Gaofeng Wang ([email protected])