Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals

American Journal of Respiratory and Critical Care Medicine

Volumn 192, Issue 11, 2015, Pages 1335-1344

  Beck, James M ^a,b   Schloss, Patrick D ^c   Venkataraman, Arvind ^c   Twigg, Homer ^d   Jablonski, Kathleen A ^e   Bushman, Frederic D ^f   Campbell, Thomas B ^a   Charlson, Emily S ^g   Collman, Ronald G ^g   Crothers, Kristina ^h   Curtis, Jeffrey L ^c,i   Drews, Kimberly L ^e   Flores, Sonia C ^a   Fontenot, Andrew P ^a   Foulkes, Mary A ^e   Frank, Ian ^g   Ghedin, Elodie ^f   Huang, Laurence ^j   Lynch, Susan V ^j   Morris, Alison ^k   Palmer, Brent E ^a   Schmidt, Thomas M ^c   Sodergren, Erica ^l   Weinstock, George M ^l   Young, Vincent B ^c   more..

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

^b Eastern Colorado Veterans Health Care System   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d INDIANA UNIVERSITY   (United States)

^e GEORGE WASHINGTON UNIVERSITY   (United States)

^f Department of Microbiology ^*  (United States)

^g UNIVERSITY OF PENNSYLVANIA   (United States)

^h UNIVERSITY OF WASHINGTON   (United States)

ⁱ VA ANN ARBOR HEALTHCARE SYSTEM   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

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

^l JACKSON LABORATORY   (United States)

more..

Author keywords

Bronchoalveolar lavage; Bronchoscopy; HIV infection; Lung; Microbiome

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; RNA 16S;

ACTINOMYCES; ADULT; AGED; ARTICLE; ATOPOBIUM; CD4 LYMPHOCYTE COUNT; COMMUNITY STRUCTURE; CONTROLLED STUDY; FEMALE; GRANULICATELLA; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HUMAN TISSUE; LAVAGE; LUNG LAVAGE; LUNG MICROBIOME; MAJOR CLINICAL STUDY; MALE; MICROBIAL DIVERSITY; MICROBIOME; MICROFLORA; MOUTH FLORA; NONHUMAN; ORAL WASH; POPULATION ABUNDANCE; PRIORITY JOURNAL; RNA SEQUENCE; ROTHIA; STREPTOCOCCUS; TAXONOMIC IDENTIFICATION; VEILLONELLA; BRONCHOALVEOLAR LAVAGE FLUID; CLINICAL TRIAL; COHORT ANALYSIS; COMPARATIVE STUDY; HIV INFECTIONS; LUNG; MICROBIOLOGY; MIDDLE AGED; MOUTH; MULTICENTER STUDY; PROSPECTIVE STUDY;

ADULT; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; BRONCHOALVEOLAR LAVAGE FLUID; COHORT STUDIES; FEMALE; HIV INFECTIONS; HUMANS; LUNG; MALE; MICROBIOTA; MIDDLE AGED; MOUTH; PROSPECTIVE STUDIES;

EID: 84946580818     PISSN: 1073449X     EISSN: 15354970     Source Type: Journal    
DOI: 10.1164/rccm.201501-0128OC     Document Type: Article

References (40)

1. Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res 2012;160:258-266.
2. Twigg HL III, Morris A, Ghedin E, Curtis JL, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM, et al.; Lung HIV Microbiome Project. Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respir Med 2013; 1:354-356.
3. 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.
4. Beck JM. ABCs of the lung microbiome. Ann Am Thorac Soc 2014;11: S3-S6.
5. 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.
6. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, et al.; Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013;187:1067-1075.
7. Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, et al.; Lung HIV Microbiome Project. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med 2013;187:1110-1117.
8. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS 2010;14:9-59.
9. 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.
10. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. Plos One 2011;6: e16384.
11. Sze MA, Hogg JC, Sin DD. Bacterial microbiome of lungs in COPD. Int J Chron Obstruct Pulmon Dis 2014;9:229-238.
12. Tunney MM, Einarsson GG, Wei L, Drain M, Klem ER, Cardwell C, Ennis M, Boucher RC, Wolfgang MC, Elborn JS. 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.
13. Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, et al.; National Heart, Lung, and Blood Institute's Asthma Clinical Research Network. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 2011;127: 372-381.e1, 3.
14. Huang YJ. Asthma microbiome studies and the potential for new therapeutic strategies. Curr Allergy Asthma Rep 2013;13: 453-461.
15. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, et al. Disordered microbial communities in asthmatic airways. Plos One 2010;5: e8578.
16. Dickson RP, Erb-Downward JR, Freeman CM, Walker N, Scales BS, Beck JM, Martinez FJ, Curtis JL, Lama VN, Huffnagle GB. Changes in the lung microbiome following lung transplantation include the emergence of two distinct Pseudomonas species with distinct clinical associations. Plos One 2014; 9: e97214.
17. Willner DL, Hugenholtz P, Yerkovich ST, Tan ME, Daly JN, Lachner N, Hopkins PM, Chambers DC. Reestablishment of recipientassociated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. Am J Respir Crit Care Med 2013;187:640-647.
18. Borewicz K, Pragman AA, Kim HB, Hertz M, Wendt C, Isaacson RE. Longitudinal analysis of the lung microbiome in lung transplantation. FEMS Microbiol Lett 2013;339:57-65.
19. 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.
20. Stressmann FA, Connett GJ, Goss K, Kollamparambil TG, Patel N, Payne MS, Puddy V, Legg J, Bruce KD, Rogers GB. The use of culture-independent tools to characterize bacteria in endo-tracheal aspirates from pre-term infants at risk of bronchopulmonary dysplasia. J Perinat Med 2010;38:333-337.
21. Beeton ML, Maxwell NC, Davies PL, Nuttall D, McGreal E, Chakraborty M, Spiller OB, Kotecha S. Role of pulmonary infection in the development of chronic lung disease of prematurity. Eur Respir J 2011;37:1424-1430.
22. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012;109:5809-5814.
23. Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, Li JZ, LiPuma JJ. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc 2013;10:179-187.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75: 7537-7541.
25. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. Plos One 2011;6: e27310.
26. Hubbell SP. Neutral theory in community ecology and the hypothesis of functional equivalence. Funct Ecol 2005;19:166-172.
27. Yue JC, Clayton MK. A similarity measure based on species proportions. Commun Stat Theory Methods 2005;34:2123-2131.
28. Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol 2001;26:32-46.
29. Wade WG. The oral microbiome in health and disease. Pharmacol Res 2013;69:137-143.
30. Razzouk S, Termechi O. Host genome, epigenome, and oral microbiome interactions: toward personalized periodontal therapy. J Periodontol 2013;84:1266-1271.
31. Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SV, Huang L. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol 2012;50:2995-3002.
32. Sharifzadeh A, Khosravi AR, Shokri H, Asadi Jamnani F, Hajiabdolbaghi M, Ashrafi Tamami I. Oral microflora and their relation to risk factors in HIV1 patients with oropharyngeal candidiasis. J Mycol Med 2013;23:105-112.
33. Dang AT, Cotton S, Sankaran-Walters S, Li CS, Lee CY, Dandekar S, Paster BJ, George MD. Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients. BMC Microbiol 2012;12:153.
34. 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.
35. Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, 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.
36. Stressmann FA, Rogers GB, Klem ER, Lilley AK, Donaldson SH, Daniels TW, Carroll MP, Patel N, Forbes B, Boucher RC, et al. Analysis of the bacterial communities present in lungs of patients with cystic fibrosis from American and British centers. J Clin Microbiol 2011;49:281-291.
37. Huffnagle GB. The microbiota and allergies/asthma. Plos Pathog 2010;6: e1000549.
38. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014;20:159-166.
39. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature 2014;509: 357-360.
40. Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. Plos One 2012;7: e42786.