biostudies-literatureJabeen MFNIHR Oxford Biomedical Research CentreMedical Research CouncilWellcome TrustNational Institute for Health Research Southampton Biomedical Research CentreNIHR Primary Care Research Network2966-2980https://www.ebi.ac.uk/biostudies/studies/S-EPMC7617782biostudies-literatureUnknown79(11)<h4>Background</h4>The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.<h4>Methods</h4>Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link.<h4>Results</h4>TAllergySpecies-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma.PMC7617782211050/Z/18/z211050Donachie GSanderson NDMarchi EStreet TLTine MAzim APavord IDJabeen MFChauhan ALau LCKHowarth PHBarber CHinks TSCKlenerman PBrown TfalseSpecies-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma.<h4>Background</h4>The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.<h4>Methods</h4>Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link.<h4>Results</h4>T2024-01-01T00:00:00Z2024 Nov2025-07-25T03:08:19.371Z2025-07-25T03:08:19.371ZS-EPMC76177823912790810.1111/all.16269