Functional Metagenomics of the Bronchial Microbiome in COPD

Millares, Laura; Ferrari, Rafaela Gomes; Gallego, Miguel; Pomares, Xavier; García-Núñez, Marian; Montón, Concepción; Capilla, Sílvia; Monsó, Eduard; Moya, Andrés

doi:10.1371/journal.pone.0144448

Cited by 44 publications

(47 citation statements)

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“…KEEG (Kyoto Encyclopedia of Genes and Genomes) pathway [36] was used to identify metagenomic contents. Abundance profiles of functional annotations were obtained and differences in the functional genomic content were evaluated after normalizing the abundances of each category to the total number of proteins predicted for each sample [37]. …”

Section: Methodsmentioning

confidence: 99%

The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

et al. 2017

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BackgroundThe bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was obtained by 16S rRNA gene amplification and sequencing, and functional capabilities through PICRUSt.ResultsThirteen patients with severe asthma were included and provided 11 bronchial biopsies (BB) and 12 bronchial aspirates (BA) suitable for sequence analyses. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria showed relative abundances (RAs) over 5% in BB, a cutoff that was reached by Streptococcus and Prevotella at genus level. Legionella genus attained a median RA of 2.7 (interquartile range 1.1–4.7) in BB samples. In BA a higher RA of Fusobacteria was found, when compared with BB [8.7 (5.9–11.4) vs 4.2 (0.8–7.5), p = 0.037], while the RA of Proteobacteria was lower in BA [4.3 (3.7–6.5) vs 17.1 (11.2–33.4), p = 0.005]. RA of the Legionella genus was also significantly lower in BA [0.004 (0.001–0.02) vs. 2.7 (1.1–4.7), p = 0.005]. Beta-diversity analysis confirmed the differences between the microbial communities in BA and BB (R2 = 0.20, p = 0.001, Adonis test), and functional analysis revealed also statistically significant differences between both types of sample on Metabolism, Cellular processes, Human diseases, Organismal systems and Genetic information processing pathways.ConclusionsThe microbiota in the bronchial mucosa of severe asthma has a specific pattern that is not accurately represented in bronchial secretions, which must be considered a different niche of bacteria growth.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0933-6) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

et al. 2017

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“…In the absence of direct methods to clearly separate bacterial cells from host cells, bioinformatic methods can be used that focus on non-human prokaryotic sequences reads such as the MG-RAST pipeline (18). Few studies to date have applied meta-genomics or meta-transcriptomics to study the respiratory microbiome (66-68), but this situation is likely to change.…”

Section: Future Directions and Unanswered Questionsmentioning

confidence: 99%

Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions

Huang

Erb-Downward

Dickson

et al. 2017

Translational Research

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In the past several years, advances in sequencing platforms and bioinformatics have transformed our understanding of the relationship between microbial ecology and human health. Both the normal and diseased lung are host to hundreds of bacterial genera, blurring the lines between “colonization” and “infection”. However whereas in health the respiratory microbiome is determined primarily by the dynamic balance of immigration and elimination, in chronic disease conditions become much more favorable for the reproduction of resident bacteria. Recent studies demonstrate that the microbiota of the COPD lung differ from the healthy lung although significant intra- and inter-subject heterogeneity are still present with variation impacted by factors such as disease stage and inhaled medications. Changes in the relative abundance of specific bacterial taxa during COPD exacerbations have also been noted although further longitudinal analyses are needed to ascertain the malleability and resilience of this ecological system and its role in the occurrence and frequency of exacerbations. Whether patients with a “frequent exacerbator” phenotype possess specific or greater alterations in their airway microbiome that predispose them to recurrent exacerbations as compared to non-frequent exacerbators needs to be determined. While recent data suggest that the presence of bacteria has the potential to influence the host immune response, a key challenge in the next few years will be to continue to move beyond descriptive studies to define the clinical relevance of differences in lung microbiota associated with COPD.

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“…The highest level in the KEGG categories was presented as level 1, followed by level 2. Level 3 reflected the KEGG pathways, and level 4 (gene expression level) contained expression of specific genes with entail enzyme commission (EC) numbers (Millares et al, 2015;Yu and Zhang, 2012). The other pipeline parameters were kept at default settings, minimum alignment length of 15, maximum e-value of 10 À5 and minimum identity of 60%.…”

Section: Rna Extraction and Metatranscriptomic Sequencingmentioning

confidence: 99%

Temperature regulates methane production through the function centralization of microbial community in anaerobic digestion

Lin

Vrieze

et al. 2016

Bioresource Technology

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Functional Metagenomics of the Bronchial Microbiome in COPD

Cited by 44 publications

References 49 publications

The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions

Temperature regulates methane production through the function centralization of microbial community in anaerobic digestion

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