The microbiome and the lung

Annals of the American Thoracic Society

Volumn 11, Issue , 2014, Pages S227-S232

  Cui, Lijia ^a,b   Morris, Alison ^c   Huang, Laurence ^d   Beck, James M ^e,f   Twigg, Homer L ^g   Von Mutius, Erika ^h   Ghedin, Elodie ^a,c  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b Tsinghua University   (China)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Health Care System   (United States)

^f UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^g INDIANA UNIVERSITY   (United States)

^h LUDWIG MAXIMILIANS UNIVERSITY   (Germany)

Author keywords

Asthma; Chronic obstructive pulmonary disease; HIV AIDS; Lung; Microbiome

Indexed keywords

GAMMA INTERFERON; INTERNAL TRANSCRIBED SPACER; RNA 16S; TUMOR NECROSIS FACTOR ALPHA;

ACINETOBACTER; ASPERGILLUS; ASTHMA; BRONCHOSCOPE; CANDIDA; CHRONIC OBSTRUCTIVE LUNG DISEASE; CRYPTOCOCCUS; CYSTIC FIBROSIS; DENSITY GRADIENT CENTRIFUGATION; FUSOBACTERIUM; GENE SEQUENCE; HAEMOPHILUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HYGIENE HYPOTHESIS; LACTOCOCCUS LACTIS; LUNG; LUNG MICROBIOME; MICROBIAL COMMUNITY; MICROBIAL CONTAMINATION; MICROBIOME; NONHUMAN; POLYMERASE CHAIN REACTION; PORPHYROMONAS; PREVALENCE; PREVOTELLA; PSEUDOMONAS; RESPIRATORY TRACT ALLERGY; REVIEW; STREPTOCOCCUS; SYSTEMIC MYCOSIS; VEILLONELLA; LUNG DISEASE; MICROBIOLOGY; MICROFLORA;

HUMANS; LUNG; LUNG DISEASES; MICROBIOTA;

EID: 84911496142     PISSN: 23296933     EISSN: 23256621     Source Type: Journal    
DOI: 10.1513/AnnalsATS.201402-052PL     Document Type: Review

References (42)

1. Proctor LM. The human microbiome project in 2011 and beyond. Cell Host Microbe 2011;10:287-291.
2. Mitreva M. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-214.
3. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006;444:1022-1023.
4. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027-1031.
5. Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res 2012;160:258-266.
6. Huang YJ, Charlson ES, Collman RG, Colombini-Hatch S, Martinez FD, Senior RM. The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report. Am J Respir Crit Care Med 2013;187:1382-1387.
7. Kiley JP. Advancing respiratory research. Chest 2011;140:497-501.
8. Ege MJ, Mayer M, Normand A-C, Genuneit J, Cookson WO, Braun- Fahrländer C, Heederik D, Piarroux R, von Mutius E. Exposure to environmental microorganisms and childhood asthma. N Engl J Med 2011;364:701-709.
9. Huse SM, Ye Y, Zhou Y, Fodor AA. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 2012;7:e34242.
10. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLOS Comput Biol 2010;6:e1000667.
11. 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.
12. Li K, Bihan M, Methé BA. Analyses of the stability and core taxonomic memberships of the human microbiome. PLoS ONE 2013;8:e63139.
13. Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med 2013;5:63.
14. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 2011;8:761-763.
15. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013;187:1067-1075.
16. 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.
17. Delwart E. A roadmap to the human virome. PLoS Pathog 2013;9:e1003146.
18. Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med 2013;187:1110-1117.
19. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B. Analysis of the lung microbiome in the "healthy " smoker and in COPD. PLoS ONE 2011;6:e16384.
20. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012;109:5809-5814.
21. Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, Fligner CL, Singh PK. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA 2012;109:13769-13774.
22. Sze MA, Dimitriu PA, Hayashi S, Elliott WM, McDonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC. The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012;185:1073-1080.
23. Iliev ID, Underhill DM. Striking a balance: fungal commensalism versus pathogenesis. Curr Opin Microbiol 2013;16:366-373.
24. Hawksworth DL. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 2001;105:1422-1432.
25. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010;6:e1000713.
26. Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med 2012;186:536-545.
27. Delhaes L, Monchy S, Fréalle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community-implications for therapeutic management. PLoS ONE 2012;7:e36313.
28. Sethi S, Murphy TF. Infection in the pathogenesis and course of chronic obstructive pulmonary disease. N Engl J Med 2008;359:2355-2365.
29. Limper AH, Thomas CF, Anders RA, Leof EB. Interactions of parasite and host epithelial cell cycle regulation during Pneumocystis carinii pneumonia. J Lab Clin Med 1997;130:132-138.
30. Morris A, Alexander T, Radhi S, Lucht L, Sciurba FC, Kolls JK, Srivastava R, Steele C, Norris KA. Airway obstruction is increased in Pneumocystis-colonized human immunodeficiency virus-infected outpatients. J Clin Microbiol 2009;47:3773-3776.
31. Shipley TW, Kling HM, Morris A, Patil S, Kristoff J, Guyach SE, Murphy JE, Shao X, Sciurba FC, Rogers RM. Persistent Pneumocystis colonization leads to the development of chronic obstructive pulmonary disease in a nonhuman primate model of AIDS. J Infect Dis 2010;202:302-312.
32. Christensen PJ, Preston AM, Ling T, Du M, Fields WB, Curtis JL, Beck JM. Pneumocystis murina infection and cigarette smoke exposure interact to cause increased organism burden, development of airspace enlargement, and pulmonary inflammation in mice. Infect Immun 2008;76:3481-3490.
33. Strachan DP. Hay fever, hygiene, and household size. BMJ 1989;299:1259-1260.
34. von Hertzen L, Hyvärinen A, Laatikainen T, Mäkelä MJ, Nevalainen A, Vartiainen E, Haahtela T. Risk of atopy associated with microbial components in house dust. Ann Allergy Asthma Immunol 2010;104: 269-270.
35. Pakarinen J, Hyvärinen A, Salkinoja-Salonen M, Laitinen S, Nevalainen A, Mäkelä MJ, Haahtela T, Von Hertzen L. Predominance of Gram-positive bacteria in house dust in the low-allergy risk Russian Karelia. Environ Microbiol 2008;10:3317-3325.
36. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, Von Mutius E, Farrall M, Lathrop M, Cookson WO. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010;363:1211-1221.
37. Holbreich M, Genuneit J, Weber J, Braun-Fahrländer C, Waser M, von Mutius E. Amish children living in northern Indiana have a very low prevalence of allergic sensitization. J Allergy Clin Immunol 2012;129:1671-1673.
38. Schaub B, Liu J, Höppler S, Schleich I, Huehn J, Olek S, Wieczorek G, Illi S, von Mutius E. Maternal farm exposure modulates neonatal immune mechanisms through regulatory T cells. J Allergy Clin Immunol 2009;123:774-782.
39. Pfefferle PI, Büchele G, Blümer N, Roponen M, Ege MJ, Krauss-Etschmann S, Genuneit J, Hyvärinen A, Hirvonen M-R, Lauener R. Cord blood cytokines are modulated by maternal farming activities and consumption of farm dairy products during pregnancy: the pasture study. J Allergy Clin Immunol 2010;125:108-115.
40. Debarry J, Garn H, Hanuszkiewicz A, Dickgreber N, Blümer N, von Mutius E, Bufe A, Gatermann S, Renz H, Holst O. Acinetobacter lwoffii and Lactococcus lactis strains isolated from farm cowsheds possess strong allergy-protective properties. J Allergy Clin Immunol 2007;119:1514-1521.
41. Conrad ML, Ferstl R, Teich R, Brand S, Blümer N, Yildirim AÖ, Patrascan CC, Hanuszkiewicz A, Akira S, Wagner H. Maternal TLR signaling is required for prenatal asthma protection by the nonpathogenic microbe Acinetobacter lwoffii f78. J Exp Med 2009;206:2869-2877.
42. Beck JM. ABCs of the lung microbiome. Ann Am Thorac Soc 2014;11:S1-S3.