Sputum Microbiome Is Associated with 1-Year Mortality after Chronic Obstructive Pulmonary Disease Hospitalizations

Filho, Fernando Sergio Leitão; Alotaibi, Nawaf M.; Ngan, David A.; Tam, Sheena; Yang, Julia; Hollander, Zsuzsanna; Chen, Virginia; FitzGerald, J. Mark; Nislow, Corey; Leung, Janice M.; Man, S. F. Paul; Sin, Don D.

doi:10.1164/rccm.201806-1135oc

Cited by 108 publications

(81 citation statements)

References 46 publications

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“…Details regarding the PCR amplification of the 16S rRNA gene V4 region were previously reported [27]. The cecal microbiome was determined by polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region using the Illumina MiSeq 1 platform (2 x 250 bp) [28].…”

Section: Microbiome Profilingmentioning

confidence: 99%

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

et al. 2020

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RationaleChronic smoke exposure is associated with weight loss in patients with Chronic Obstructive Pulmonary Disease (COPD). However, the biological contribution of chronic smoking and sex on the cecal microbiome has not been previously investigated. MethodsAdult male, female and ovariectomized mice were exposed to air (control group) or smoke for six months using a standard nose-only smoke exposure system. DNA was extracted from the cecal content using the QIAGEN QIAamp® DNA Mini Kit. Droplet digital PCR was used to generate total 16S bacterial counts, followed by Illumina MiSeq® analysis to determine microbial community composition. The sequencing data were resolved into Amplicon Sequence Variants and analyzed with the use of QIIME2 ® . Alpha diversity measures (Richness, Shannon Index, Evenness and Faith's Phylogenetic Diversity) and beta diversity (based on Bray-Curtis distances) were assessed and compared according to smoke exposure and sex.

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Section: Microbiome Profilingmentioning

confidence: 99%

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

et al. 2020

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“…The airway microbiome in chronic obstructive pulmonary disease (COPD) has been well studied in the last decade. The airway microbiome differs between health and COPD[1–3], shifts during exacerbations[4–6], associates with airway inflammation[5, 7] and predicts 1-year mortality of hospitalized exacerbation patients[8], all suggesting the implication of airway microbiome in COPD pathogenesis. Despite advances, the precise role of airway microbiome in COPD remains incompletely understood.…”

Section: Introductionmentioning

confidence: 99%

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels

Wang

Liu

Wang

et al. 2020

Preprint

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Little is known about the species and strain-level diversity of the airway microbiome, and its implication in chronic obstructive pulmonary disease (COPD).Here we report the first comprehensive analysis of the COPD airway microbiome at species and strain-levels. The full-length 16S rRNA gene was sequenced from sputum in 98 stable COPD patients and 27 age-matched healthy controls, using the ‘third-generation’ Pacific Biosciences sequencing platform.Individual species within the same genus exhibited reciprocal relationships with COPD and disease severity. Species dominant in health can be taken over by another species within the same genus in GOLD IV patients. Such turnover was also related to enhanced symptoms and exacerbation frequency. Ralstonia mannitolilytica, an opportunistic pathogen, was significantly increased in COPD frequent exacerbators. There were inflammatory phenotype-specific associations of microbiome at the species-level. One group of four pathogens including Haemophilus influenzae and Moraxella catarrhalis, were specifically associated with sputum mediators for neutrophilic inflammation. Another group of seven species, including Tropheryma whipplei, showed specific associations with mediators for eosinophilic inflammation. Strain-level detection uncovered three non-typeable H. influenzae strains PittEE, PittGG and 86-028NP in the airway microbiome, where PittGG and 86-028NP abundances may inversely predict eosinophilic inflammation. The full-length 16S data augmented the power of functional inference and led to the unique identification of butyrate-producing and nitrate reduction pathways as significantly depleted in COPD.Our analysis uncovered substantial intra-genus heterogeneity in the airway microbiome associated with inflammatory phenotypes and could be of clinical importance, thus enabled a refined view of the airway microbiome in COPD.“Take-home” messageThe species-level analysis using the ‘third-generation’ sequencing enabled a refined view of the airway microbiome and its relationship with clinical outcome and inflammatory phenotype in COPD.

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“…provided a state‐of‐the‐art review, describing the methods, the potential application and limitations of current molecular techniques to interrogate the lower airway microbiome in COPD . Although the airway microbiome may have a broad‐ranging impact in COPD patients, clinical translation of these techniques is closest in the setting of acute exacerbations where airway microbiome research has unveiled sputum microbial markers of mortality following hospitalizations . In one study, the presence of Staphylococcus species (which are pathogens in airways) and the absence of Veillonella species, which are normal commensals in the airways, were associated with a >10‐fold increase in the risk of 1‐year mortality .…”

Section: Emerging Areas In the Era Of ‘Omics’mentioning

confidence: 99%

“…Although the airway microbiome may have a broad‐ranging impact in COPD patients, clinical translation of these techniques is closest in the setting of acute exacerbations where airway microbiome research has unveiled sputum microbial markers of mortality following hospitalizations . In one study, the presence of Staphylococcus species (which are pathogens in airways) and the absence of Veillonella species, which are normal commensals in the airways, were associated with a >10‐fold increase in the risk of 1‐year mortality . In the near future, the airway microbiome may become a treatable trait in COPD.…”

Section: Emerging Areas In the Era Of ‘Omics’mentioning

confidence: 99%

Contemporary Concise Review 2019: Chronic obstructive pulmonary disease

Sin

2020

Respirology

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Sputum Microbiome Is Associated with 1-Year Mortality after Chronic Obstructive Pulmonary Disease Hospitalizations

Cited by 108 publications

References 46 publications

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels

Contemporary Concise Review 2019: Chronic obstructive pulmonary disease

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