Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions

Yan, Zhengzheng; Chen, Boxuan; Yang, Yuqiong; Yi, Xinzhu; Wei, Mingyuan; Ecklu-Mensah, Gertrude; Buschmann, Mary M.; Liu, Haiyue; Gao, Jingyuan; Liang, Weijie; Liu, Xiaomin; Yang, Junhao; Ma, Wei; Liang, Zhenyu; Wang, Fengyan; Chen, Dandan; Wang, Lingwei; Shi, Weijuan; Stämpfli, Martin R.; Pan, Li; Gong, Shenhai; Chen, Xia; Shu, Wen‐Sheng; El-Omar, Emad; Gilbert, Jack A.; Zhou, Hongwei; Chen, Rongchang; Wang, Zhang

doi:10.1038/s41564-022-01196-8

Cited by 57 publications

(48 citation statements)

References 91 publications

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“…after a 6-month treatment with a probiotics-based toothpaste in association with probiotics-based chewing gum containing bacteria belonging to the Lactobacillus and Bifidobacterium genera [ 41 ]. In terms of potential therapeutic interventions targeting airway dysbiosis, reducing airway concentration levels of indole-3-acetic acid (IAA), derived from Lactobacillus spp., upregulated interleukin-22 signaling and epithelial cell apoptosis pathways in COPD [ 42 ]. In the same study, the authors observed an increase in local IAA levels with a subsequent restoration of their airway protective effects in mice following intranasal inoculation of two airway lactobacilli.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community

et al. 2023

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Lower airway dysbiosis contributes to disease pathogenesis in respiratory diseases. However, little is known regarding the microbiota of lower airways or the oral cavity of healthy young persons. To address this gap, 25 healthy persons (24.3 ± 3.3 years; 52% females; no current smokers) underwent bronchoscopy during which bronchial brushing (BB) and bronchoalveolar lavage (BAL) fluid were collected. Prior to the procedure, an oral wash (OW) sample was also obtained. Microbiome analyses (16S rRNA locus) were performed (alpha- and beta-diversity, taxa annotations, and predicted functional metagenomic profiles) according to the airway compartment (BB, BAL, and OW). The greatest microbial richness was observed in OW and the lowest in BB (p < 0.001). Microbial communities differed significantly across compartments (p < 0.001), especially between BB and OW. Taxa analyses showed a significantly higher abundance of Firmicutes (BB: 32.7%; BAL: 31.4%) compared to OW (20.9%) (p < 0.001). Conversely, Proteobacteria predominated in OW (27.9%) as opposed to BB (7.0%) and BAL (12.5%) (p < 0.001), mostly due to a greater abundance of the bacteria in the Haemophilus genus in the OW (p < 0.001). The lower airway microbiota (BB and BAL) is significantly different from the OW microbiota in healthy young persons with respect to microbial diversity, taxa profiles, and predicted function.

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Section: Discussionmentioning

confidence: 99%

Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community

et al. 2023

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“…In the largest study of its kind to date, Yan et al performed metagenomics profiling of induced sputum samples in 72 patients with COPD and 18 healthy control subjects 21 . They also performed metabolomic and transcriptomic profiling of sputum specimens in a vast majority of these individuals.…”

Section: Airway Microbiome In Copd and Other Lung Diseasesmentioning

confidence: 99%

“…Using the sputum metagenome, the investigators found that modules for bacterial transport system and amino acid biosynthesis were enriched in COPD samples; whereas modules for energy metabolism and breakdown of amino acids were depleted in COPD samples. Thus, the sputum metagenome suggested that the COPD airway promote amino acid anabolism (rather than catabolism) relative to the healthy airways 21 . These data were largely confirmed on sputum metabolomics, which showed that COPD samples were enriched for metabolites of amino acids, carbohydrates and steroids.…”

Section: Airway Microbiome In Copd and Other Lung Diseasesmentioning

confidence: 99%

Chronic Obstructive Pulmonary Disease and the Airway Microbiome: What Respirologists Need to Know

Sin¹

2023

Tuberc Respir Dis

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Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. The lower airways contain a rich and diverse microbiome, which may play a significant regulatory role in both health and disease. In COPD, the microbiome becomes perturbed, causing dysbiosis. Increased representation of members in the Proteobacteria phylum and certain members in the Firmicutes phylum has been associated with increased risk of exacerbations and mortality. Therapies such as inhaled corticosteroids and azithromycin may modulate the airway microbiome or its metabolites in patients with COPD. This paper provides an up-to-date overview of the airway microbiome and its importance in the pathophysiology of COPD and as potential therapeutic target in the future.

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“…Integrative multi-omics has been applied to unravel disease mechanisms and host-microbe interactions in chronic obstructive pulmonary disease. 3 , 5 …”

Section: Integrative Omics For Better Understanding Of Asthma Endotyp...mentioning

confidence: 99%

“…A combination of omic datasets can provide a significantly enhanced and holistic picture of interactions across the components underlying the pathophysiology of disease processes. 1 , 3 , 4 , 5 With rapid advances in modern machine learning, a suite of approaches has become available to integrate these high-dimensional multi-modal datasets. An important distinction here is between artificial intelligence (AI) and machine learning.…”

Section: Introductionmentioning

confidence: 99%

Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning

Ray¹,

Das²,

Wenzel³

2022

Cell Reports Medicine

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Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions

Cited by 57 publications

References 91 publications

Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community

Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community

Chronic Obstructive Pulmonary Disease and the Airway Microbiome: What Respirologists Need to Know

Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning

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