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Short term dynamics of the sputum microbiome among COPD patients.

ABSTRACT: Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. The complexity of the lung microbial community in COPD patients has been highlighted in recent years. Evidence suggests that transplantation, medications, age, and disease severity influence microbial community membership. However, the dynamics of the lung microbiome in stable COPD patients remain poorly understood. In this study, we completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on replicate sputum samples collected from 4 former smokers with COPD (Stage 2) within a 2-day time period. Samples from each individual over the two-day period were similar based on ?-diversity, principle component analysis and taxonomy at the phyla and genera level. Sputum samples from COPD patients were also collected between 2-9 months of follow-up. Data suggest an increased variability of the sputum microbiota when comparing samples collected ? 3 months compared to those collected ? 4 months; however, no statistically significant shifts in the abundance (>2-fold) of taxa between the two time points was observed. Bacterial composition and the number of operational taxonomic units (OTUs) remained similar over time. Results from this study suggest that the sputum microbiome is relatively stable in clinically stable COPD patients (Stage 2). This study furthers our understanding of the dynamics of the lung microbiome in COPD patients.

SUBMITTER: Sinha R

PROVIDER: S-EPMC5843169 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Short term dynamics of the sputum microbiome among COPD patients.

Sinha Rohita R Weissenburger-Moser Lisa A LA Clarke Jennifer L JL Smith Lynette M LM Heires Art J AJ Romberger Debra J DJ LeVan Tricia D TD

PloS one 20180308 3

Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. The complexity of the lung microbial community in COPD patients has been highlighted in recent years. Evidence suggests that transplantation, medications, age, and disease severity influence microbial community membership. However, the dynamics of the lung microbiome in stable COPD patients remain poorly understood. In this study, we completed a longitudinal 16S ...[more]

PMID: 29518088

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Project description:BackgroundMost empirical studies tend to focus on microbiome dynamics within hosts or microbiome compositional differences between hosts over short periods. However, there is still a dearth of formal models that allow us to investigate the observed short-term dynamics of microbiomes under a unified ecological and evolutionary framework. In our previous study, we developed a computational agent-based neutral framework that simulates microbiome dynamics spanning many host generations with the added dimension of a genealogy of hosts. Although this long-term framework revealed interesting microbial diversity patterns under a simple but plausible evolutionary process and provided a platform for future elaboration of more complex systems, it does not allow us to explore microbiome dynamics within a single host generation.MethodsIn this paper, we developed a computational, agent-based, forward-time framework of microbiome dynamics within a single host generation. As we have done under our neutral long-term models, we incorporate neutral processes of environmental microbiome assembly and microbe acquisition from parents and environment. We also incorporate a Moran genealogical model of hosts, so that the dynamics of microbiome evolution can be studied within a single host generation. Furthermore, we allow host subpopulation structure and host migration to affect microbiome recruitment.ResultsWe show that microbiome diversity within hosts increases monotonically with increases in environmental contribution, while microbiome diversity between hosts increases with increasing parental inheritance. Host population division and dispersal limitation under high host contribution further shaped the patterns by elevating microbiome differences between hosts and depressing microbial diversity within hosts. Microbiome diversity within the whole population showed strong temporal stability regardless of the modes of microbiome acquisition and subpopulation structures.ConclusionsWe present a computational framework that integrates various processes including host genealogy, microbe recruitment, and host dispersal limitation acting on the short-term dynamics of microbiomes. Our framework demonstrates that the neutral dynamics of microbiomes within a population of hosts is strongly influenced by transmission mode and shared environment.

Project description:BackgroundIt is not known whether environmental gamma radiation measured in US cities has detectable adverse health effects. We assessed whether short-term exposure to gamma radiation emitted from ambient air particles [gamma particle activity (PRγ)] is associated with reduced pulmonary function in chronic obstructive pulmonary disease (COPD) patients.ObjectiveWe hypothesize that the inhalation of gamma radiation emitted from ambient air particles may be associated with reduced pulmonary function in individuals with COPD.MethodsIn 125 patients with COPD from Eastern Massachusetts who had up to 4 seasonal one-week assessments of particulate matter ≤2.5 μm (PM2.5), black carbon (BC), and sulfur followed by spirometry. The US EPA continuously monitors ambient gamma (γ) radiation including γ released from radionuclides attached to particulate matter that is recorded as 9 γ-energy spectra classes (i = 3-9) in counts per minute (CPMγ) in the Boston area (USA). We analyzed the associations between ambient and indoor PRγi (up to one week) and pre and post-bronchodilator (BD) forced expiratory volume in 1 s (FEV1) and with forced vital capacity (FVC) using mixed-effects regression models. We estimated indoor PRγi using the ratio of the indoor-to-outdoor sulfur in PM2.5 as a proxy for infiltration of ambient radionuclide-associated particles.ResultsOverall, exposures to ambient and indoor PRγi were associated with a similar decrease in pre- and post-BD FEV1 and FVC. For example, ambient PRγ3 exposure averaged from the day of pulmonary function testing through the previous 3 days [IQR of 55.1 counts per minute (CPMγ)] was associated with a decrease in pre-BD FEV1 of 21.0 ml (95%CI: -38.5 to -3.0 ml; p < 0.01) and pre-BD FVC of 27.5 ml [95% confidence interval (CI): -50.7 to -5.0 ml; p < 0.01] with similar effects adjusting for indoor and outdoor BC and PM2.5.ConclusionOur results show that short-term ambient and indoor exposures to environmental gamma radiation associated with particulate matter are associated with reduced pre- and post-BD pulmonary function in patients with COPD.

Dataset Information

Short term dynamics of the sputum microbiome among COPD patients.

Publications

Short term dynamics of the sputum microbiome among COPD patients.

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