Severe asthma (SA) is a heterogeneous condition characterized by multiple phenotypes, each characterized by different endotypes. Understanding the mechanisms occurring in the lungs of children with SA can help in understanding pathogenesis and in providing the most effective therapeutic strategies. This article describes microbiota, metabolites, and soluble immune components assessed in bronchoalveolar lavage (BAL) fluids from children with severe asthma (n = 20) and age-matched disease controls (n = 10). The article includes: (i) the protocol used to process BAL samples for 16S rRNA gene amplicon sequencing, metabolomic profiling and immune components assays; (ii) the bioinformatics steps applied to 16S rRNA and metabolomics dataset; (iii) an overview of the raw 16S rRNA gene amplicon sequencing data, presented as ASV and affiliation tables, raw data from untargeted metabolomics and the abundances of each of the eighty eight metabolites annotated with the highest confidence level, and concentrations of seventy three cytokines and of total IgG, IgA and IgE. Each dataset is available in the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae) with respective DOI: MICROBIOTA: 10.57745/LL3TFW, METABOLITES: 10.57745/1L8VRI, IMMUNE COMPONENTS: 10.57745/JOOGRQThese datasets provide valuable resources for further investigating the molecular mechanisms underlying severe asthma in children and its trajectories. They also offer the potential to identify a local signature of severe asthma through complementary multi-omics analyses and to discover local biomarkers associated with asthma endotypes. Datasets can also be reused to compare with other cohorts (children or adults) or to serve as reference datasets for other pulmonary diseases.

Severe asthma (SA) is a heterogeneous condition characterized by multiple phenotypes, each characterized by different endotypes. Understanding the mechanisms occurring in the lungs of children with SA can help in understanding pathogenesis and in providing the most effective therapeutic strategies. This article describes microbiota, metabolites, and soluble immune components assessed in bronchoalveolar lavage (BAL) fluids from children with severe asthma (n = 20) and age-matched disease controls (n = 10). The article includes: (i) the protocol used to process BAL samples for 16S rRNA gene amplicon sequencing, metabolomic profiling and immune components assays; (ii) the bioinformatics steps applied to 16S rRNA and metabolomics dataset; (iii) an overview of the raw 16S rRNA gene amplicon sequencing data, presented as ASV and affiliation tables, raw data from untargeted metabolomics and the abundances of each of the eighty eight metabolites annotated with the highest confidence level, and concentrations of seventy three cytokines and of total IgG, IgA and IgE. Each dataset is available in the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae) with respective DOI: MICROBIOTA: 10.57745/LL3TFW, METABOLITES: 10.57745/1L8VRI, IMMUNE COMPONENTS: 10.57745/JOOGRQ These datasets provide valuable resources for further investigating the molecular mechanisms underlying severe asthma in children and its trajectories. They also offer the potential to identify a local signature of severe asthma through complementary multi-omics analyses and to discover local biomarkers associated with asthma endotypes. Datasets can also be reused to compare with other cohorts (children or adults) or to serve as reference datasets for other pulmonary diseases.