Functional metagenomics of the bronchial microbiome in COPD

PLoS ONE

Volumn 10, Issue 12, 2015, Pages

  Millares, Laura ^a,b,c,d   Pérez Brocal, Vicente ^e,f,g   Ferrari, Rafaela ^e,f,g,i   Gallego, Miguel ^h   Pomares, Xavier ^b,h   García Núñez, Marian ^a,b,c,d   Montón, Concepción ^b,h   Capilla, Silvia ^h   Monsó, Eduard ^b,c,h   Moya, Andrés ^e,f,g  

^a Unit of Clinical Trials   (Spain)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d IrsiCaixa Aids Research Institute   (Spain)

^e Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana   (Spain)

^f CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^g UNIVERSITY OF VALENCIA   (Spain)

^h Parc Taulí Hospital Universitari   (Spain)

ⁱ STATE UNIVERSITY OF LONDRINA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

16S RRNA GENE; ACTINOBACTERIA; AGED; ARTICLE; BACTERIAL GENE; BRONCHIAL MICROBIOME; BRONCHUS MUCOSA; BRONCHUS SECRETION; CHRONIC OBSTRUCTIVE LUNG DISEASE; CONTROLLED STUDY; DISEASE EXACERBATION; DISEASE SEVERITY; FEMALE; FIRMICUTES; GENE AMPLIFICATION; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; HUMAN; MAJOR CLINICAL STUDY; MALE; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PROTEOBACTERIA; PSEUDOMONAS AERUGINOSA; PYROSEQUENCING; SPUTUM ANALYSIS; STREPTOCOCCUS; DISEASE COURSE; GENETICS; LUNG; METABOLISM; METAGENOME; MICROFLORA; MIDDLE AGED; PATHOLOGY;

AGED; DISEASE PROGRESSION; FEMALE; HUMANS; LUNG; MALE; METAGENOME; METAGENOMICS; MICROBIOTA; MIDDLE AGED; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; RNA, RIBOSOMAL, 16S;

EID: 84955503679     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0144448     Document Type: Article

References (49)

1. Decramer M, Janssens W, Miravitlles M. Chronic obstructive pulmonary disease. Lancet. 2012; 379: 1341-1351. doi: 10.1016/S0140-6736(11)60968-9 PMID: 22314182
2. Sethi S, Murphy TF. Infection in the pathogenesis and course of chronic obstructive pulmonary disease. N Engl J Med. 2008; 359: 2355-2365. doi: 10.1056/NEJMra0800353 PMID: 19038881
3. Rangelov K, Sethi S. Role of infections. Clin Chest Med. 2014; 35: 87-100. doi: 10.1016/j.ccm.2013. 09.012 PMID: 24507839
4. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, et al. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Omics J Integr Biol. 2010; 14: 9-59. doi: 10.1089/omi.2009.0100
5. Pragman AA, Kim HB, Reilly CS, Wendt C, Isaacson RE. The lung microbiome in moderate and severe chronic obstructive pulmonary disease. PloS One. 2012; 7: e47305. doi: 10.1371/journal.pone. 0047305 PMID: 23071781
6. Millares L, Ferrari R, Gallego M, Garcia-Nuñez M, Pérez-Brocal V, Espasa M, et al. Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. Eur J Clin Microbiol Infect Dis Off Publ Eur Soc Clin Microbiol. 2014; 33: 1101-1111. doi: 10.1007/s10096-013-2044-0
7. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014; 52: 2813-2823. doi: 10. 1128/JCM.00035-14 PMID: 24850358
8. Davenport M, Poles J, Leung JM, Wolff MJ, Abidi WM, Ullman T, et al. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2014; 20: 723-731. doi: 10. 1097/MIB.0000000000000011 PMID: 24583479
9. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004; 32: D277-280. doi: 10.1093/nar/gkh063 PMID: 14681412
10. Carr R, Borenstein E. Comparative analysis of functional metagenomic annotation and the mappability of short reads. PloS One. 2014; 9: e105776. doi: 10.1371/journal.pone.0105776 PMID: 25148512
11. Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010; 2010: pdb.prot5368. doi: 10.1101/pdb.prot5368
12. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013; 31: 814-821. doi: 10.1038/nbt.2676 PMID: 23975157
13. Meyer F, Trimble WL, Chang EB, Handley KM. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biol. 2012; 13: 169. doi: 10.1186/ gb4042 PMID: 23013527
14. Meyer F, Paarmann D, D'Souza M, Olson R, Glass E, Kubal M, et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9: 386. doi: 10.1186/1471-2105-9-386 PMID: 18803844
15. Gallego M, Pomares X, Espasa M, Castañer E, Solé M, Suárez D, et al. Pseudomonas aeruginosa isolates in severe chronic obstructive pulmonary disease: characterization and risk factors. BMC Pulm Med. 2014; 14: 103. doi: 10.1186/1471-2466-14-103 PMID: 24964956
16. Available from: http://www.goldcopd.org/. From the Global Strategy for the Diagnosis, Management and Prevention of COPD, Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2013.
17. Pomares X, Montón C, Espasa M, Casabon J, Monsó E, Gallego M. Long-term azithromycin therapy in patients with severe COPD and repeated exacerbations. Int J Chron Obstruct Pulmon Dis. 2011; 6: 449-456. doi: 10.2147/COPD.S23655 PMID: 22003290
18. Anthonisen NR, Manfreda J, Warren CP, Hershfield ES, Harding GK, Nelson NA. Antibiotic therapy in exacerbations of chronic obstructive pulmonary disease. Ann Intern Med. 1987; 106: 196-204. PMID: 3492164
19. Rodriguez-Roisin R. Toward a consensus definition for COPD exacerbations. Chest. 2000; 117: 398S-401S. PMID: 10843984
20. Standardization of spirometry-1987 update. Statement of the American Thoracic Society. Am Rev Respir Dis. 1987; 136: 1285-1298. doi: 10.1164/ajrccm/136.5.1285 PMID: 3674589
21. Celli BR, Cote CG, Marin JM, Casanova C, Montes de Oca M, Mendez RA, et al. The body-mass index, airflow obstruction, dyspnea, and exercise capacity index in chronic obstructive pulmonary disease. N Engl J Med. 2004; 350: 1005-1012. doi: 10.1056/NEJMoa021322 PMID: 14999112
22. Garcia-Nuñez M, Millares L, Pomares X, Ferrari R, Pérez-Brocal V, Gallego M, et al. Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease. J Clin Microbiol. 2014; 52: 4217-4223. doi: 10.1128/JCM.01967-14 PMID: 25253795
23. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75: 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
24. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7: 335-336. doi: 10. 1038/nmeth.f.303 PMID: 20383131
25. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72: 5069-5072. doi: 10.1128/AEM.03006-05 PMID: 16820507
26. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009; 37: D141-145. doi: 10.1093/nar/gkn879 PMID: 19004872
27. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinforma Oxf Engl. 2010; 26: 2460-2461. doi: 10.1093/bioinformatics/btq461
28. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinforma Oxf Engl. 2010; 26: 266-267. doi: 10.1093/ bioinformatics/btp636
29. Niu B, Fu L, Sun S, Li W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010; 11: 187. doi: 10.1186/1471-2105-11-187 PMID: 20388221
30. Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PloS One. 2008; 3: e2527. doi: 10.1371/journal.pone.0002527 PMID: 18575584
31. Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984; 11: 265-70.
32. Shannon CE. The mathematical theory of communication. 1963. MD Comput Comput Med Pract. 1997; 14: 306-317.
33. Bray JR, Curtis JT. An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957; 27: 325-349.
34. Tunney MM, Einarsson GG, Wei L, Drain M, Klem ER, Cardwell C, et al. Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation. Am J Respir Crit Care Med. 2013; 187: 1118-1126. doi: 10.1164/rccm.201210-1937OC PMID: 23348972
35. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. 2012; 109: 5809-5814. doi: 10.1073/pnas.1120577109 PMID: 22451929
36. Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, et al. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PloS One. 2012; 7: e45001. doi: 10.1371/journal.pone.0045001 PMID: 23049765
37. van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, et al. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J. 2011; 5: 780-791. doi: 10.1038/ismej.2010.175 PMID: 21151003
38. Iwai S, Huang D, Fong S, Jarlsberg LG, WorodriaW, Yoo S, et al. The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients. PloS One. 2014; 9: e95726. doi: 10.1371/journal.pone.0095726 PMID: 24752365
39. Greenblum S, Carr R, Borenstein E. Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species. Cell. 2015; 160: 583-594. doi: 10.1016/j.cell.2014.12.038 PMID: 25640238
40. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012; 490: 55-60. doi: 10.1038/nature11450 PMID: 23023125
41. Wei X, Yan X, Zou D, Yang Z, Wang X, Liu W, et al. Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach. BMC Gastroenterol. 2013; 13: 175. doi: 10.1186/1471-230X-13-175 PMID: 24369878
42. Chaffin DO, Taylor D, Skerrett SJ, Rubens CE. Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung. PloS One. 2012; 7: e41329. doi: 10.1371/journal.pone.0041329 PMID: 22876285
43. Seidl K, Müller S, François P, Kriebitzsch C, Schrenzel J, Engelmann S, et al. Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus. BMC Microbiol. 2009; 9: 95. doi: 10.1186/ 1471-2180-9-95 PMID: 19450265
44. Seidl K, Stucki M, Ruegg M, Goerke C, Wolz C, Harris L, et al. Staphylococcus aureus CcpA affects virulence determinant production and antibiotic resistance. Antimicrob Agents Chemother. 2006; 50: 1183-1194. doi: 10.1128/AAC.50.4.1183-1194.2006 PMID: 16569828
45. Shelburne SA, Davenport MT, Keith DB, Musser JM. The role of complex carbohydrate catabolism in the pathogenesis of invasive streptococci. Trends Microbiol. 2008; 16: 318-325. doi: 10.1016/j.tim. 2008.04.002 PMID: 18508271
46. Shelburne SA, Olsen RJ, Suber B, Sahasrabhojane P, Sumby P, Brennan RG, et al. A combination of independent transcriptional regulators shapes bacterial virulence gene expression during infection. PLoS Pathog. 2010; 6: e1000817. doi: 10.1371/journal.ppat.1000817 PMID: 20333240
47. Barreiro E, Fermoselle C, Mateu-Jimenez M, Sánchez-Font A, Pijuan L, Gea J, et al. Oxidative stress and inflammation in the normal airways and blood of patients with lung cancer and COPD. Free Radic Biol Med. 2013; 65: 859-871. doi: 10.1016/j.freeradbiomed.2013.08.006 PMID: 23954470
48. de Torres JP, Bastarrika G, Wisnivesky JP, Alcaide AB, Campo A, Seijo LM, et al. Assessing the relationship between lung cancer risk and emphysema detected on low-dose CT of the chest. Chest. 2007; 132: 1932-1938. doi: 10.1378/chest.07-1490 PMID: 18079226
49. Schroedl C, Kalhan R. Incidence, treatment options, and outcomes of lung cancer in patients with chronic obstructive pulmonary disease. Curr Opin Pulm Med. 2012; 18: 131-137. doi: 10.1097/MCP. 0b013e32834f2080 PMID: 22262137