Immunity Inflammation and Disease · 2023 · 16 citations · 39 references
Life SciencesImmunologyMicrobiologyBacteriologyInflammationMicrobiome ResearchMicrobial Community ProfilingMicrobiome BiomarkersMicrobiome CompositionMicrobiome DiversityMicrobiome DysbiosisRespiratory MicrobiomeAmplicon Sequence VariantsBiomass Smoke ExposureDifferential Abundance AnalysisInflammatory Cytokine ProductionLung DiseasesLung MicrobiomeSputum MicrobiologyTobacco Smoking
INTRODUCTION: Lung microbiome dysbiosis affects the immune system balance and promotes lung inflammation. We aimed to characterize and compare the lung bacteriome composition and the cytokine profile in women with normal lung function exposed to risk factors for chronic lung diseases (tobacco smoking and biomass-burning smoke exposure). METHODS: We included women with biomass-burning smoke exposure (BE, n = 11) and current smokers women (TS, n = 10). The bacteriome composition was performed in induced sputum, sequencing the 16 rRNA gene. Cytokine levels were measured using enzyme-linked immunosorbent assay multiplex assay in the supernatant of induced sputum. For quantitative variables, we used medians and minimum and maxim values. For the amplicon sequence variants (ASV) differential abundance testing between groups. RESULTS: At the taxa level, the phylum Proteobacteria was found in a higher proportion in the TS group concerning BE (p = .045); however, after the false discovery rate adjustment, this difference was not retained (p = .288). We found a higher concentration of IL-1β in the TS group than in the BE group (248.6 vs. 177.9 pg/mL, p = .010). Women with high biomass-burning smoke exposure in an hour per day had a positive correlation with the abundance of Bacteroidota (ρ = 0.71, p = .014) and Fusobacteriota (ρ = 0.73, p = .011). FEV1/FVC had a positive correlation with an abundance of Bacteroidota, Proteobacteria, and Fusobacteria (ρ = 0.74, p = .009, ρ = 0.85, p = .001, and ρ = 0.83, p = .001, respectively). In tobacco smoking, women had a positive correlation (ρ = 0.77, p = .009) between cigarettes per day and Firmicutes' abundance. CONCLUSION: Compared to biomass-burning smoke-exposed women, current smokers have poor lung function and high levels of IL-1β in sputum. Women with biomass-burning smoke exposure present an increased abundance of Bacteroidota and Fusobacteriota.
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DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen et al. · Nature Methods · 2016 · 36.3K citations
Normalization and microbial differential abundance strategies depend upon data characteristics
Sophie Weiss, Zhenjiang Zech Xu, Shyamal D. Peddada et al. · Microbiome · 2017 · 2.2K citations · Full text
Life Sciences, Biology, Ecology +15