scholarly journals The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0248967
Author(s):  
Einar M. H. Martinsen ◽  
Tomas M. L. Eagan ◽  
Elise O. Leiten ◽  
Ingvild Haaland ◽  
Gunnar R. Husebø ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Large Scale ◽  
Study Groups ◽  
Taxonomic Composition ◽  
Shannon Index ◽  
Chronic Obstructive ◽  
Sample Type ◽  
Obstructive Pulmonary Disease ◽  
Alpha And Beta Diversity ◽  
Inhaled Steroids

Background The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD). Methods Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids. Results The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids. Conclusion Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.

scholarly journals Ranking the Biases: The Choice of OTUs vs. ASVs in 16S rRNA Amplicon Data Analysis Has Stronger Effects On Diversity Measures Than Rarefaction and Similarity Threshold

2021 ◽  
Author(s):  
Marlène Chiarello ◽  
Mark McCauley ◽  
Sébastien Villéger ◽  
Colin R Jackson
Keyword(s):  
16S Rrna ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Taxonomic Composition ◽  
Shannon Index ◽  
Minimal Impact ◽  
Alpha And Beta Diversity ◽  
Methodological Choices ◽  
Similarity Threshold

Abstract BackgroundAdvances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from the classification and downstream analyses of traditional operational taxonomic units (OTUs), and towards the usage of amplicon sequence variants (ASVs). While ASVs have several inherent properties that make them desirable compared to OTUs, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. ResultsWe compared the respective influences of using ASVs vs. OTU-based pipelines, rarefaction of the community table, and OTU similarity threshold (97% vs. 99%) on the ecological signals detected in freshwater invertebrate and environmental (sediment, seston) 16S rRNA data sets, determining the effects on alpha diversity, beta diversity and taxonomic composition. While the choice of OTU vs. ASV pipeline significantly influenced unweighted alpha and beta diversities and changed the ecological signal detected, weighted indices such as the Shannon index, Bray-Curtis dissimilarity, and weighted Unifrac scores were not impacted by the pipeline followed. By comparison, OTU threshold and rarefaction had a minimal impact effect on all measurements, although rarefaction improved overall signals, especially in OTU-based datasets. The identification of major classes and genera identified revealed significant discrepancies across methodologies. ConclusionWe provide a list of recommendations for the analysis of 16S rRNA amplicon data. We notably recommend the use of ASVs when analyzing alpha-diversity patterns, especially in species-rich or environmental samples. Abundance weighted alpha- and beta-diversity indices should also be preferred compared to ones based on the presence-absence of biological units.

scholarly journals Understanding racial differences of COPD patients with an ecological model: two large cohort studies in the US and Korea

2021 ◽  
Vol 12 ◽  
pp. 204062232098245
Author(s):  
Hye Yun Park ◽  
Hyun Lee ◽  
Danbee Kang ◽  
Hye Sook Choi ◽  
Yeong Ha Ryu ◽  
...  
Keyword(s):  
Racial Differences ◽  
Large Scale ◽  
Ecological Model ◽  
Prevalence Ratio ◽  
Poor Quality ◽  
Smoking History ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Copd Patients ◽  
The Us

Background: There are limited data about the racial difference in the characteristics of chronic obstructive pulmonary disease (COPD) patients who are treated at clinics. We aimed to compare sociodemographic and clinical characteristics between US and Korean COPD patients using large-scale nationwide COPD cohorts. Methods: We used the baseline demographic and clinical data of COPD patients aged 45 years or older with at least a 10 pack-per year smoking history from the Korean COPD Subtype Study (KOCOSS, n = 1686) cohort (2012–2018) and phase I (2008–2011) of the US Genetic Epidemiology of COPD (COPDGene) study ( n = 4477, 3461 were non-Hispanic whites [NHW], and 1016 were African Americans [AA]). Results: Compared to NHW, AA had a significantly lower adjusted prevalence ratio (aPR) of cough >3 months (aPR: 0.67; 95% CI [confidence interval]: 0.60–0.75) and phlegm >3 months (aPR: 0.78, 95% CI: 0.70–0.86), but higher aPR of dyspnea (modified Medical Round Council scale ⩾2) (aPR: 1.22; 95% CI: 1.15–1.29), short six-minute walk distance (<350 m) (aPR: 1.98; 95% CI: 1.81–2.14), and poor quality of life (aPR: 1.10; 95% CI: 1.05–1.15). Compared to NHW, Koreans had a significantly lower aPR of cough >3 months (aPR: 0.53; 95% CI: 0.47–0.59), phlegm >3 months (aPR: 0.75; 95% CI: 0.67–0.82), dyspnea (aPR: 0.72; 95% CI: 0.66–0.79), and moderate-to-severe acute exacerbation in the previous year (aPR: 0.73; 95% CI: 0.65–0.82). NHW had the highest burden related to chronic bronchitis symptoms and cardiovascular diseases related to comorbidities. Conclusion: There are substantial differences in sociodemographic characteristics, clinical presentation, and comorbidities between COPD patients from the KOCOSS and COPDGene, which might be caused by interactions between various intrapersonal, interpersonal, and environmental factors of the ecological model. Thus, a broader and more comprehensive approach would be necessary to understand the racial differences of COPD patients.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

SLOWING THE DETERIORATION OF ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE OBSERVED DURING BRONCHODILATOR THERAPY BY ADDING INHALED CORTICOSTEROIDS: A 4-YEAR PROSPECTIVE STUDY

PEDIATRICS ◽  
1994 ◽  
Vol 94 (2) ◽  
pp. 269-270
Author(s):  
Peter Cvietusa ◽  
Joseph Spahn ◽  
William R. Otto
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Pulmonary Function ◽  
Pulmonary Disease ◽  
Bronchial Hyperreactivity ◽  
Rapid Decline ◽  
Chronic Obstructive ◽  
Exacerbation Rate ◽  
Obstructive Pulmonary Disease ◽  
Bronchodilator Therapy ◽  
Inhaled Steroids

Purpose of the Study. To determine if the deterioration in lung function, seen in adults with asthma or chronic obstructive pulmonary disease (COPD), could be reversed or slowed by the addition of inhaled beclomethasone. Many short-term studies have shown the benefits of inhaled steroids in asthma; in particular, their ability to improve pulmonary function, decrease bronchial hyperreactivity, and reduce symptoms. Few studies have evaluated the long-term effects of inhaled steroids on the clinical course of either asthma or COPD. Methods. This report is an extension of a 2-year study that followed 160 patients with asthma or COPD on bronchodilator therapy alone. From this group, 56 patients who displayed a rapid decline in pulmonary function (FEV1 ≥ 80 ml/year) and a high exacerbation rate (≥1/year) were selected to receive additional treatment with beclomethasone dipropionate 400 µg two times daily over 4 years. FEV1 and airways responsiveness to histamine were measured every 6 months and at 1 and 13 months upon completion of the study. Peak flows and symptom scores were recorded weekly, and compliance, inhaler technique, and adverse affects were monitored every 3 months. Findings. During the first 6 months of beclomethasone treatment, both groups showed a significant improvement in pre- and postbronchodilator FEV1 with the most significant change noted in the asthma group. Thereafter, the FEV1 began to decline again, as it had in the first 2 years of the study, but at a rate that was 33% slower. In addition to slowing the decline in FEV1, inhaled beclomethasone resulted in a substantial decrease in the degree of bronchial hyperreactivity, and peak flow rates improved.

scholarly journals Environmental Temperatures Affect the Gastrointestinal Microbes of the Chinese Giant Salamander

2021 ◽  
Vol 12 ◽  
Author(s):  
Lifeng Zhu ◽  
Wei Zhu ◽  
Tian Zhao ◽  
Hua Chen ◽  
Chunlin Zhao ◽  
...  
Keyword(s):  
Potential Effect ◽  
Shannon Index ◽  
Effect Of Temperature ◽  
Sample Type ◽  
Gastrointestinal Microbiome ◽  
Unifrac Distance ◽  
Alpha And Beta Diversity ◽  
Significant Difference ◽  
Unweighted Unifrac ◽  
Sample Time

An increasing number of studies have shown that warming also influences the animal gut microbiome (altering the community structure and decreasing its diversity), which might further impact host fitness. Here, based on an analysis of the stomach and gut (the entire intestine: from the anterior intestine to the cloaca) microbiome in laboratory larva of giant salamanders (Andrias davidianus) under different living water temperatures (5, 15, and 25°C) at two sample time points (80 and 330 days after the acclimation), we investigated the potential effect of temperature on the gastrointestinal microbiome community. We found the significant Interaction between sampling time and temperature, or type (stomach and gut) on Shannon index in the gastrointestinal microbiome of the giant salamanders. We also found the significant difference in Shannon index among temperature groups within the same sample type (stomach or gut) at each sample time. 10% of variation in microbiome community could be explained by temperature alone in the total samples. Both the stomach and gut microbiomes displayed the highest similarity in the microbiome community (significantly lowest pairwise unweighted Unifrac distance) in the 25-degree group between the two sampling times compared to those in the 5-degree and 15-degree groups. Moreover, the salamanders in the 25°C treatment showed the highest food intake and body mess compared to that of other temperature treatments. A significant increase in the abundance of Firmicutes in the gastrointestinal microbiome on day 330 with increasing temperatures might be caused by increased host metabolism and food consumption. Therefore, we speculate that the high environmental temperature might indirectly affect both alpha and beta diversity of the gastrointestinal microbiome.

scholarly journals Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
T. Goolam Mahomed ◽  
R. P. H. Peters ◽  
M. Allam ◽  
A. Ismail ◽  
S. Mtshali ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Small Sample ◽  
Chronic Obstructive ◽  
Shotgun Metagenomics ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition ◽  
Disease States ◽  
Dna And Rna ◽  
Lung Microbiome ◽  
Copd Patients

AbstractChronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

scholarly journals Regenerative pharmacology for COPD: breathing new life into old lungs

Thorax ◽  
2019 ◽  
Vol 74 (9) ◽  
pp. 890-897 ◽  
Author(s):  
John-Poul Ng-Blichfeldt ◽  
Reinoud Gosens ◽  
Charlotte Dean ◽  
Mark Griffiths ◽  
Matthew Hind
Keyword(s):  
Large Scale ◽  
Biologically Active ◽  
Health Concern ◽  
Chronic Obstructive ◽  
Small Airways ◽  
Obstructive Pulmonary Disease ◽  
Molecular Control ◽  
Mild Disease ◽  
Peripheral Airway ◽  
Alveolar Tissue

Chronic obstructive pulmonary disease (COPD) is a major global health concern with few effective treatments. Widespread destruction of alveolar tissue contributes to impaired gas exchange in severe COPD, and recent radiological evidence suggests that destruction of small airways is a major contributor to increased peripheral airway resistance in disease. This important finding might in part explain the failure of conventional anti-inflammatory treatments to restore lung function even in patients with mild disease. There is a clear need for alternative pharmacological strategies for patients with COPD/emphysema. Proposed regenerative strategies such as cell therapy and tissue engineering are hampered by poor availability of exogenous stem cells, discouraging trial results, and risks and cost associated with surgery. An alternative therapeutic approach is augmentation of lung regeneration and/or repair by biologically active factors, which have potential to be employed on a large scale. In favour of this strategy, the healthy adult lung is known to possess a remarkable endogenous regenerative capacity. Numerous preclinical studies have shown induction of regeneration in animal models of COPD/emphysema. Here, we argue that given the widespread and irreversible nature of COPD, serious consideration of regenerative pharmacology is necessary. However, for this approach to be feasible, a better understanding of the cell-specific molecular control of regeneration, the regenerative potential of the human lung and regenerative competencies of patients with COPD are required.

scholarly journals Increased CD11b and Decreased CD62L in Blood and Airway Neutrophils from Long-Term Smokers with and without COPD

2020 ◽  
Vol 12 (6) ◽  
pp. 480-489
Author(s):  
Marit Stockfelt ◽  
Karin Christenson ◽  
Anders Andersson ◽  
Lena Björkman ◽  
Médea Padra ◽  
...  
Keyword(s):  
Surface Density ◽  
Defense Mechanism ◽  
Ex Vivo ◽  
Study Groups ◽  
Lower Surface ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Host Defense Mechanism ◽  
Blood Neutrophils

There is incomplete mechanistic understanding of the mobilization of neutrophils in the systemic and local compartment in smokers with chronic obstructive pulmonary disease (COPD). In this pilot study, we characterized how the adhesion molecules CD11b and CD62L, surface markers indicative of priming, are altered as neutrophils extravasate, and whether surface density of CD11b and CD62L differs between long-term tobacco smokers (LTS) with and without COPD compared with healthy never-smokers (HNS). Unstimulated blood neutrophils from LTS with (<i>n</i> = 5) and without (<i>n</i> = 9) COPD displayed lower surface density of CD62L compared with HNS (<i>n</i> = 8). In addition, surface density of CD11b was higher in bronchoalveolar lavage (BAL) neutrophils from LTS without COPD compared with those with COPD and HNS. Moreover, in BAL neutrophils from all study groups, CD62L was lower compared with matched blood neutrophils. In addition, BAL neutrophils responded with a further decrease in CD62L to ex vivo TNF stimulation. Thus, neutrophils in the airway lumen display a higher state of priming than systemic neutrophils and bear the potential to be further primed by local cytokines even with no smoking or the presence of COPD, findings that may represent a universal host defense mechanism against local bacteria. Moreover, systemic neutrophils are primed in LTS regardless of COPD. Further studies in larger materials are warranted to determine whether the priming of neutrophils is protective against COPD or merely preceding it.

Sign in / Sign up

Export Citation Format

Share Document