DOI: 10.5061/dryad.7m0cfxpwr
title: Lung microbiota analyses in asthma mouse model

description: Background: Asthma is a frequent chronic inflammatory bronchial disease
 affecting more than 300 million patients worldwide, 70% of whom secondary
 to allergy. The diversity of asthmatic endotypes contributes to their
 complexity. Many factors, such as the environment, allergen sensitization
 pathways associate with microbiota, influence asthma natural course and
 explain its phenotypic heterogeneity. Here, we compared a mouse model of
 house dust mite (HDM)-induced allergic asthma sensitized via various
 routes for the clinical features of asthma, immune responses, the lung
 barrier and dysbiosis. Method: Mice were sensitized HDM by oral, nasal or
 percutaneous routes. Lung function, barrier integrity, immune response and
 microbiota composition were analyzed. Results: Severe impairment of
 respiratory function was observed in the mice sensitized by the nasal and
 cutaneous paths. It was associated with epithelial dysfunction
 characterized by an increased permeability secondary to junction protein
 disruption. Conversely, such sensitization paths induced a mixed
 eosinophilic and neutrophilic inflammatory response with high IL-17
 airways secretion. In contrast, oral sensitized mice showed a mild
 impairment of respiratory function. Epithelial dysfunction was lighter
 with increased mucus production but conserved epithelial junctions. Lung
 Th2 and eosinophilic inflammation were observed. Considering lung
 microbiota, sensitization provoked a significant loss diversity. At the
 genus level, Cutibacterium, Acinetobacter, Streptococcus and Lactobacillus
 were found to be modulated according to the sensitization pathway. An
 increase in anti-inflammatory microbiota metabolites was observed in the
 oral group. Conclusion: Our study highlights the strong involvement of the
 sensitization route in allergic asthma physiopathology and the critical
 phenotypic diversity in a mouse model.
description: Analysis
 of microbiota composition. Bacterial DNA was extracted from BAL pellets according to the manufacturer’s instructions
 (Macherey Nagel, genomic DNA from tissue, Nucleospin
 Tissue). The
 microbiota composition was
 analyzed by 16S sequencing
 with permission from
 Biofortis (Saint-Herblain, France). Raw sequencing data were obtained from
 a single Illumina MiSeq run as 250 bp paired-end reads targeting the V3-V4
 region (Primers : Bakt_341F 5′-CCTACGGGNGGCWGCAG-3′,Bakt_805R
 5′ GACTACHVGGGTATCTAATCC-3) of the 16S rDNA gene. Reads were processed
 with microSysMics (https://bio.tools/microSysMics), a workflow built
 around the QIIME2 toolbox, chaining softwares in order to automatize
 metabarcoding analysis. PCR primers and remaining Illumina adapters were
 removed with Cutadapt. ASVs inference and count estimation were performed
 with dada2 using a trimming length of 220 and default parameters. We used
 a Naive Bayes Classifier pre-trained on the SILVA 99% reference database
 (Release 138) to assign ASVs to taxa.
description: Reads were processed with microSysMics
 (https://bio.tools/microSysMics), a workflow built around the QIIME2
 toolbox, chaining softwares in order to automatize metabarcoding
 analysis.