The microbiome of the upper airways: focus on chronic rhinosinusitis

World Allergy Organization Journal

Volumn 8, Issue 1, 2015, Pages

  Chalermwatanachai, Thanit ^a,b   Velásquez, Leydi Carolina ^a,c   Bachert, Claus ^a,d  

^a GHENT UNIVERSITY HOSPITAL   (Belgium)

^b PHRAMONGKUTKLAO HOSPITAL   (Thailand)

^c UNIVERSIDAD INDUSTRIAL DE SANTANDER   (Colombia)

^d KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALLERGIC RHINITIS; ARTICLE; BACTERIUM CULTURE; BURKHOLDERIA CEPACIA; CAMPYLOBACTER; CAPNOCYTOPHAGA; CARNOBACTERIUM; CHRONIC RHINOSINUSITIS; CITROBACTER; CORYNEBACTERIUM; CURTOBACTERIUM; CYANOBACTERIUM; CYSTIC FIBROSIS; ENTEROBACTER; ENTEROCOCCUS; FUSOBACTERIUM; GRANULICATELLA; HAEMOPHILUS; HELICOBACTER; HUMAN; LACTOBACILLUS SAKEI; LEPTOTRICHIA; MICROBIOME; MICROCOCCUS; MICROFLORA; MORAXELLA; MYCOBACTERIUM; NEISSERIA; NONHUMAN; OCHROBACTRUM; PEPTOSTREPTOCOCCUS; PORPHYROMONAS; PREVOTELLA; PRIORITY JOURNAL; PROPIONIBACTERIUM ACNES; PSEUDOMONAS AERUGINOSA; RHIZOBIUM; ROTHIA; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS; STENOTROPHOMONAS; STREPTOCOCCUS ANGINOSUS; STREPTOCOCCUS CONSTELLATUS; STREPTOCOCCUS INTERMEDIUS; STREPTOCOCCUS MILLERI; VALIDATION PROCESS; VEILLONELLA;

EID: 84938914631     PISSN: None     EISSN: 19394551     Source Type: Journal    
DOI: 10.1186/s40413-014-0048-6     Document Type: Article

References (73)

1. Herbst T, Sichelstiel A, Schar C, Yadava K, Burki K, Cahenzli J, McCoy K, Marsland BJ, Harris NL: Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am J Respir Crit Care Med 2011, 184:198-205.
2. Hormannsperger G, Clavel T, Haller D: Gut matters: microbe-host interactions in allergic diseases. J Allergy Clin Immunol 2012, 129:1452-1459.
3. Strachan DP: Hay fever, hygiene, and household size. BMJ 1989, 299:1259-1260.
4. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R: The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol 2012, 129:1204-1208.
5. Human Microbiome Project Consortium: A framework for human microbiome research. Nature 2012, 486(7402):215-221.
6. Goldstein-Daruech N, Cope EK, Zhao KQ, Vukovic K, Kofonow JM, Doghramji L, Gonzalez B, Chiu AG, Kennedy DW, Palmer JN, Leid JG, Kreindler JL, Cohen NA: Tobacco smoke mediated induction of sinonasal microbial biofilms. PLoS One 2011, 6:e15700.
7. Huang YJ: Asthma microbiome studies and the potential for new therapeutic strategies. Curr Allergy Asthma Rep 2013, 13(5):453-461.
8. Huang YJ, Lynch SV: The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med 2011, 5:809-821.
9. Lynch SV, Bruce KD: The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med 2013, 3:a009738.
10. Suzaki H, Watanabe S, Pawankar R: Rhinosinusitis and asthma-microbiome and new perspectives. Curr Opin Allergy Clin Immunol 2013, 13:45-49.
11. Marsland BJ: Regulation of inflammatory responses by the commensal microbiota. Thorax 2012, 67:93-94.
12. Jany JL, Barbier G: Culture-independent methods for identifying microbial communities in cheese. Food Microbiol 2008, 25:839-848.
13. Amann RI, Ludwig W, Schleifer KH: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169.
14. Vartoukian SR, Palmer RM, Wade WG: Strategies for culture of 'Unculturable' bacteria. FEMS Microbiol Lett 2010, 309:1-7.
15. Su C, Lei L, Duan Y, Zhang KQ, Yang J: Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 2012, 93:993-1003.
16. Orphan VJ, Taylor LT, Hafenbradl D, Delong EF: Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 2000, 66:700-711.
17. Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, Lynch SV: Sinus microbiome diversity depletion and corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med 2012, 4:151ra24.
18. Boase S, Foreman A, Cleland E, Tan L, Melton-Kreft R, Pant H, Hu FZ, Ehrlich GD, Wormald PJ: The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection. BMC Infect Dis 2013, 13:210.
19. Hugenholtz P, Goebel BM, Pace NR: Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998, 180:4765-4774.
20. Nocker A, Burr M, Camper AK: Genotypic microbial community profiling: a critical technical review. Microb Ecol 2007, 54:276-289.
21. Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A: Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 2000, 102:615-623.
22. Janda JM, Abbott SL: 16 s rrna gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007, 45:2761-2764.
23. Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW: Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16 s rrna gene regions. Nucleic Acids Res 2010, 38:e200.
24. von Wintzingerode F, Gobel UB, Stackebrandt E: Determination of microbial diversity in environmental samples: pitfalls of Pcr-based rrna analysis. FEMS Microbiol Rev 1997, 21:213-229.
25. Kim BS, Jeon YS, Chun J: Current status and future promise of the human microbiome. Pediatr Gastroenterol Hepatol Nutr 2013, 16:71-79.
26. Mardis ER: Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto, Calif) 2013, 6:287-303.
27. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG: Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011, 184:957-963.
28. Noverr MC, Huffnagle GB: The 'Microflora Hypothesis' of allergic diseases. Clin Exp Allergy 2005, 35:1511-1520.
29. Abrahamsson TR, Jakobsson HE, Andersson AF, Bjorksten B, Engstrand L, Jenmalm MC: Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy 2013, 44(6):842-50.
30. Bisgaard H, Li N, Bonnelykke K, Chawes BL, Skov T, Paludan-Muller G, Stokholm J, Smith B, Krogfelt KA: Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J Allergy Clin Immunol 2011, 128:646-52 e1-5.
31. Sjogren YM, Jenmalm MC, Bottcher MF, Bjorksten B, Sverremark-Ekstrom E: Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clin Exp Allergy 2009, 39:518-526.
32. Clemente JC, Ursell LK, Parfrey LW, Knight R: The impact of the gut microbiota on human health: an integrative view. Cell 2012, 148:1258-1270.
33. Toh ZQ, Anzela A, Tang ML, Licciardi PV: Probiotic therapy as a novel approach for allergic disease. Front Pharmacol 2012, 3:171.
34. Storro O, Avershina E, Rudi K: Diversity of intestinal microbiota in infancy and the risk of allergic disease in childhood. Curr Opin Allergy Clin Immunol 2013, 13:257-262.
35. West CE, Jenmalm MC, Prescott SL: The gut microbiota and its role in the development of allergic disease: a wider perspective. Clin Exp Allergy 2014. [Epub ahead of print]
36. Hansel TT, Johnston SL, Openshaw PJ: Microbes and mucosal immune responses in asthma. Lancet 2013, 381:861-873.
37. Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, Wolfgang MC: 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.
38. Zemanick ET, Sagel SD, Harris JK: The airway microbiome in cystic fibrosis and implications for treatment. Curr Opin Pediatr 2011, 23:319-324.
39. Delhaes L, Monchy S, Frealle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E, Sime-Ngando T, Chabe M, Viscogliosi E: The airway microbiota in cystic fibrosis: a complex fungal and bacterial community-implications for therapeutic management. PLoS One 2012, 7:e36313.
40. Lim YW, Schmieder R, Haynes M, Willner D, Furlan M, Youle M, Abbott K, Edwards R, Evangelista J, Conrad D, Rohwer F: Metagenomics and metatranscriptomics: windows on Cf-associated viral and microbial communities. J Cyst Fibros 2013, 12(2):154-64.
41. Zhao J, Carmody LA, Kalikin LM, Li J, Petrosino JF, Schloss PD, Young VB, LiPuma JJ: Impact of enhanced staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS One 2012, 7:e33127.
42. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ: Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 2012, 109:5809-5814.
43. Liu CM, Soldanova K, Nordstrom L, Dwan MG, Moss OL, Contente-Cuomo TL, Keim P, Price LB, Lane AP: Medical therapy reduces microbiota diversity and evenness in surgically recalcitrant chronic rhinosinusitis. Int Forum Allergy Rhinol 2013, 3(10):775-81.
44. Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, Hoffman L, Daniels TW, Patel N, Forbes B, Bruce KD: Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax 2012, 67:867-873.
45. Rogers GB, Carroll MP, Bruce KD: Studying bacterial infections through culture-independent approaches. J Med Microbiol 2009, 58:1401-1418.
46. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA: Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013, 8:e62917.
47. Rabin HR, Surette MG: The cystic fibrosis airway microbiome. Curr Opin Pulm Med 2012, 18:622-627.
48. Surette MG: The cystic fibrosis lung microbiome. Ann Am Thorac Soc 2014, 11:s61-s65.
49. Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, Hoffman NG: Rapid 16 s rrna next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One 2013, 8:e65226.
50. Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S, Cavanaugh CM: Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J 2011, 5:20-29.
51. Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, Parkins MD, Rabin HR, Surette MG: Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One 2011, 6:e22702.
52. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV: Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 2010, 5:e11044.
53. Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR: Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 2007, 104:20529-20533.
54. Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Bruce KD: Characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16 s ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 2004, 42:5176-5183.
55. Stressmann FA, Rogers GB, Chan SW, Howarth PH, Harries PG, Bruce KD, Salib RJ: Characterization of bacterial community diversity in chronic rhinosinusitis infections using novel culture-independent techniques. Am J Rhinol Allergy 2011, 25:e133-e140.
56. Feazel LM, Robertson CE, Ramakrishnan VR, Frank DN: Microbiome complexity and staphylococcus aureus in chronic rhinosinusitis. Laryngoscope 2012, 122:467-472.
57. Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, Mizunoe Y: Staphylococcus epidermidis Esp inhibits staphylococcus aureus biofilm formation and nasal colonization. Nature 2010, 465:346-349.
58. Gluck U, Gebbers JO: Ingested probiotics reduce nasal colonization with pathogenic bacteria (staphylococcus aureus, streptococcus pneumoniae, and beta-hemolytic streptococci). Am J Clin Nutr 2003, 77:517-520.
59. Nadel DM, Lanza DC, Kennedy DW: Endoscopically guided cultures in chronic sinusitis. Am J Rhinol 1998, 12:233-241.
60. Stephenson MF, Mfuna L, Dowd SE, Wolcott RD, Barbeau J, Poisson M, James G, Desrosiers M: Molecular characterization of the polymicrobial flora in chronic rhinosinusitis. J Otolaryngol Head Neck Surg 2010, 39:182-187.
61. Ramakrishnan VR, Feazel LM, Gitomer SA, Ir D, Robertson CE, Frank DN: The microbiome of the middle meatus in healthy adults. PLoS One 2013, 8:e85507.
62. Aurora R, Chatterjee D, Hentzleman J, Prasad G, Sindwani R, Sanford T: Contrasting the microbiomes from healthy volunteers and patients with chronic rhinosinusitis. JAMA Otolaryngol Head Neck Surg 2013, 139:1328-1338.
63. Frank DN, Feazel LM, Bessesen MT, Price CS, Janoff EN, Pace NR: The human nasal microbiota and staphylococcus aureus carriage. PLoS One 2010, 5:e10598.
64. Healy DY, Leid JG, Sanderson AR, Hunsaker DH: Biofilms with fungi in chronic rhinosinusitis. Otolaryngol Head Neck Surg 2008, 138:641-647.
65. Sanderson AR, Leid JG, Hunsaker D: Bacterial biofilms on the sinus mucosa of human subjects with chronic rhinosinusitis. Laryngoscope 2006, 116:1121-1126.
66. Lina G, Boutite F, Tristan A, Bes M, Etienne J, Vandenesch F: Bacterial competition for human nasal cavity colonization: role of staphylococcal Agr alleles. Appl Environ Microbiol 2003, 69:18-23.
67. Rasmussen TT, Kirkeby LP, Poulsen K, Reinholdt J, Kilian M: Resident aerobic microbiota of the adult human nasal cavity. APMIS 2000, 108:663-675.
68. Corriveau MN, Zhang N, Holtappels G, Van Roy N, Bachert C: Detection of staphylococcus aureus in nasal tissue with peptide nucleic acid-fluorescence in situ hybridization. Am J Rhinol Allergy 2009, 23:461-465.
69. Akdis CA, Bachert C, Cingi C, Dykewicz MS, Hellings PW, Naclerio RM, Schleimer RP, Ledford D: Endotypes and phenotypes of chronic rhinosinusitis: a practall document of the European Academy of Allergy and Clinical Immunology and the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol 2013, 131:1479-1490.
70. Ba L, Zhang N, Meng J, Zhang J, Lin P, Zhou P, Liu S, Bachert C: The association between bacterial colonization and inflammatory pattern in Chinese chronic rhinosinusitis patients with nasal polyps. Allergy 2011, 66:1296-1303.
71. Van Zele T, Claeys S, Gevaert P, Van Maele G, Holtappels G, Van Cauwenberge P, Bachert C: Differentiation of chronic sinus diseases by measurement of inflammatory mediators. Allergy 2006, 61:1280-1289.
72. Rolain JM, Fancello L, Desnues C, Raoult D: Bacteriophages as vehicles of the resistome in cystic fibrosis. J Antimicrob Chemother 2011, 66:2444-2447.
73. Sarowska J, Choroszy-Krol I, Regulska-Ilow B, Frej-Madrzak M, Jama-Kmiecik A: The therapeutic effect of probiotic bacteria on gastrointestinal diseases. Adv Clin Exp Med 2013, 22:759-766.