Functional Metagenomics of the Bronchial Microbiome in COPD
Publication Date
December 03, 2015
Journal
PLOS ONE
Authors
Laura Millares, Vicente Pérez Brocal, Rafaela Ferrari, Miguel Gallego, et al
Volume
10
Issue
12
Pages
e0144448
DOI
https://dx.plos.org/10.1371/journal.pone.0144448
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0144448
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26632844
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669145
Europe PMC
http://europepmc.org/abstract/MED/26632844
Web of Science
000366040000084
Scopus
84955503679
Mendeley
http://www.mendeley.com/research/functional-metagenomics-bronchial-microbiome-copd
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Mendeley | Further Information

{"title"=>"Functional metagenomics of the bronchial microbiome in COPD", "type"=>"journal", "authors"=>[{"first_name"=>"Laura", "last_name"=>"Millares", "scopus_author_id"=>"35765371600"}, {"first_name"=>"Vicente", "last_name"=>"Pérez-Brocal", "scopus_author_id"=>"7801672300"}, {"first_name"=>"Rafaela", "last_name"=>"Ferrari", "scopus_author_id"=>"56415763500"}, {"first_name"=>"Miguel", "last_name"=>"Gallego", "scopus_author_id"=>"55382766400"}, {"first_name"=>"Xavier", "last_name"=>"Pomares", "scopus_author_id"=>"16245498200"}, {"first_name"=>"Marian", "last_name"=>"García-Núñez", "scopus_author_id"=>"6507933907"}, {"first_name"=>"Concepción", "last_name"=>"Montón", "scopus_author_id"=>"6603958638"}, {"first_name"=>"Silvia", "last_name"=>"Capilla", "scopus_author_id"=>"6505858271"}, {"first_name"=>"Eduard", "last_name"=>"Monsó", "scopus_author_id"=>"55041612300"}, {"first_name"=>"Andrés", "last_name"=>"Moya", "scopus_author_id"=>"7103153137"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84955503679", "pui"=>"607883939", "doi"=>"10.1371/journal.pone.0144448", "pmid"=>"26632844", "scopus"=>"2-s2.0-84955503679", "issn"=>"19326203", "isbn"=>"1098-660X; 0095-1137"}, "id"=>"c4dc7a14-ec4f-3609-9c19-138a185a28e5", "abstract"=>"The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.", "link"=>"http://www.mendeley.com/research/functional-metagenomics-bronchial-microbiome-copd", "reader_count"=>61, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>24, "Medicine and Dentistry"=>15, "Chemical Engineering"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>5, "Economics, Econometrics and Finance"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>15}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Brazil"=>2, "United Kingdom"=>1, "Germany"=>1, "India"=>2}, "group_count"=>2}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/4314514"], "description"=>"<p>Baseline clinical characteristics.</p>", "links"=>[], "tags"=>["Metagenomics RAST server", "stability", "16 S rRNA gene amplification", "microbiome", "3.6", "quality sputum samples", "exacerbation", "COPD patients", "KEGG", "16 S data", "abundance", "vs"], "article_id"=>1618261, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Physiology", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Laura Millares", "Vicente Pérez-Brocal", "Rafaela Ferrari", "Miguel Gallego", "Xavier Pomares", "Marian García-Núñez", "Concepción Montón", "Silvia Capilla", "Eduard Monsó", "Andrés Moya"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0144448.t001"], "stats"=>{"downloads"=>3, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Baseline_clinical_characteristics_/1618261", "title"=>"Baseline clinical characteristics.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-12-03 10:18:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/4314520"], "description"=>"<p>Relative abundance of the phyla detected in stability and exacerbation samples.</p>", "links"=>[], "tags"=>["Metagenomics RAST server", "stability", "16 S rRNA gene amplification", "microbiome", "3.6", "quality sputum samples", "exacerbation", "COPD patients", "KEGG", "16 S data", "abundance", "vs"], "article_id"=>1618262, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Physiology", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Laura Millares", "Vicente Pérez-Brocal", "Rafaela Ferrari", "Miguel Gallego", "Xavier Pomares", "Marian García-Núñez", "Concepción Montón", "Silvia Capilla", "Eduard Monsó", "Andrés Moya"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0144448.t002"], "stats"=>{"downloads"=>5, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_the_phyla_detected_in_stability_and_exacerbation_samples_/1618262", "title"=>"Relative abundance of the phyla detected in stability and exacerbation samples.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-12-03 10:18:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/4314460", "https://ndownloader.figshare.com/files/4314466"], "description"=>"<div><p>The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, <i>Cell growth and Death</i> and <i>Transport and Catabolism</i> decreased in abundance [1.6 (0.2–2.3) <i>vs</i> 3.6 (3.3–6.9), p = 0.012; and 1.8 (0–3.3) <i>vs</i> 3.6 (1.8–5.1), p = 0.025 respectively], while <i>Cancer</i> and <i>Carbohydrate Metabolism</i> increased [0.8 (0–1.5) <i>vs</i> 0 (0–0.5), p = 0.043; and 7 (6.4–9) <i>vs</i> 5.9 (6.3–6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.</p></div>", "links"=>[], "tags"=>["Metagenomics RAST server", "stability", "16 S rRNA gene amplification", "microbiome", "3.6", "quality sputum samples", "exacerbation", "COPD patients", "KEGG", "16 S data", "abundance", "vs"], "article_id"=>1618265, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Physiology", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry"], "users"=>["Laura Millares", "Vicente Pérez-Brocal", "Rafaela Ferrari", "Miguel Gallego", "Xavier Pomares", "Marian García-Núñez", "Concepción Montón", "Silvia Capilla", "Eduard Monsó", "Andrés Moya"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0144448.s001", "https://dx.doi.org/10.1371/journal.pone.0144448.s002"], "stats"=>{"downloads"=>5, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_Metagenomics_of_the_Bronchial_Microbiome_in_COPD_/1618265", "title"=>"Functional Metagenomics of the Bronchial Microbiome in COPD", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-12-03 10:18:49"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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