The respiratory microbiome of HIV-infected individuals

References

• Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355–1359.
   PubMed Web of Science ®Google Scholar
• Baughman RP, Thorpe JE, Staneck J, et al. Use of the protected specimen brush in patients with endotracheal or tracheostomy tubes. Chest. 1987;91(2):233–236.
   PubMed Web of Science ®Google Scholar
• Thorpe JE, Baughman RP, Frame PT, et al. Bronchoalveolar lavage for diagnosing acute bacterial pneumonia. J Infect Dis. 1987;155(5):855–861.
   PubMed Web of Science ®Google Scholar
• Kahn FW, Jones JM. Diagnosing bacterial respiratory infection by bronchoalveolar lavage. J Infect Dis. 1987;155(5):862–869.
   PubMed Web of Science ®Google Scholar
• Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res. 2012;160(4):258–266.
   PubMed Web of Science ®Google Scholar
• Erb-Downward JR, Thompson DL, Han MK, et al. Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One. 2011;6(2):e16384.
   PubMed Web of Science ®Google Scholar
• Hilty M, Burke C, Pedro H, et al. Disordered microbial communities in asthmatic airways. PLoS One. 2010;5(1):e8578.
   PubMed Web of Science ®Google Scholar
• Barfod KK, Roggenbuck M, Hansen L, et al. The murine lung microbiome in relation to the intestinal and vaginal bacterial communities. BMC Microbiol. 2013;13:303.
   PubMed Web of Science ®Google Scholar
• Morris A, Crothers K, Beck JM, et al. An official ATS workshop report: emerging issues and current controversies in HIV-associated pulmonary diseases. Proc Am Thorac Soc. 2011;8(1):17–26.
   PubMedGoogle Scholar
• Crothers K, Thompson BW, Burkhardt K, et al. HIV-associated lung infections and complications in the era of combination antiretroviral therapy. Proc Am Thorac Soc. 2011;8(3):275–281.
   PubMedGoogle Scholar
• Crothers K, Butt AA, Gibert CL, et al. Increased COPD among HIV-positive compared to HIV-negative veterans. Chest. 2006;130(5):1326–1333.
   PubMed Web of Science ®Google Scholar
• Gingo MR, George MP, Kessinger CJ, et al. Pulmonary function abnormalities in HIV-infected patients during the current antiretroviral therapy era. Am J Respir Crit Care Med. 2010;182(6):790–796.
   PubMed Web of Science ®Google Scholar
• Dickson RP, Erb-Downward JR, Huffnagle GB. The role of the bacterial microbiome in lung disease. Expert Rev Respir Med. 2013;7(3):245–257.
   PubMed Web of Science ®Google Scholar
• Twigg HL 3rd, Morris A, Ghedin E, et al. Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respir Med. 2013;1(5):354–356.
   PubMed Web of Science ®Google Scholar
• Beck JM, Schloss PD, Venkataraman A, et al. Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals. Am J Respir Crit Care Med. 2015;192(11):1335–1344.
   PubMed Web of Science ®Google Scholar
• Lozupone C, Cota-Gomez A, Palmer BE, et al. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013;187(10):1110–1117.
   PubMed Web of Science ®Google Scholar
• Morris A, Beck JM, Schloss PD, et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013;187(10):1067–1075.
   PubMed Web of Science ®Google Scholar
• Twigg Iii, HL, Knox KS, Zhou J, et al. Effect of advanced HIV infection on the respiratory microbiome. Am J Respir Crit Care Med. 2016.doi:10.1164/rccm.201509-1875OC
   PubMed Web of Science ®Google Scholar
• Rossouw TM, Anderson R, Feldman C. Impact of HIV infection and smoking on lung immunity and related disorders. Eur Respir J. 2015;46(6):1781–1795.
   PubMed Web of Science ®Google Scholar
• Twigg HL 3rd, Knox KS. HIV-related lung disorders. Drug Discov Today Dis Mech. 2007;4(2):95–101.
   PubMedGoogle Scholar
• Brenchley JM, Knox KS, Asher AI, et al. High frequencies of polyfunctional HIV-specific T cells are associated with preservation of mucosal CD4 T cells in bronchoalveolar lavage. Mucosal Immunol. 2008;1(1):49–58.
   PubMed Web of Science ®Google Scholar
• Brenchley JM, Paiardini M, Knox KS, et al. Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections. Blood. 2008;112(7):2826–2835.
   PubMed Web of Science ®Google Scholar
• Favre D, Mold J, Hunt PW, et al. Tryptophan catabolism by indoleamine 2,3-Dioxygenase 1 alters the balance of TH17 to regulatory T Cells in HIV disease. Sci Transl Med. 2010;2(32):32ra36.
   PubMed Web of Science ®Google Scholar
• Brenchley JM, Price DA, Schacker TW, et al. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med. 2006;12(12):1365–1371.
   PubMed Web of Science ®Google Scholar
• Douek DC. Immune activation, HIV persistence, and the cure. Top Antivir Med. 2013;21(4):128–132.
   PubMedGoogle Scholar
• Segal LN, Blaser MJ. A brave new world: the lung microbiota in an era of change. Ann Am Thorac Soc. 2014;11(Suppl 1):S21–S27.
   PubMedGoogle Scholar
• Ichinohe, T, Pang IK, Kumamoto Y. et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci U S A. 2011;108(13):5354–5359.
   PubMed Web of Science ®Google Scholar
• Samuelson DR, Welsh DA, Shellito JE. Regulation of lung immunity and host defense by the intestinal microbiota. Front Microbiol. 2015;6:1085.
   PubMed Web of Science ®Google Scholar
• Wang J, Li F, Wei H, et al. Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation. J Exp Med. 2014;211(12):2397–2410.
   PubMed Web of Science ®Google Scholar
• Mammen MJ, Sethi S. COPD and the microbiome. Respirology. 2016;21:590–599.
   PubMed Web of Science ®Google Scholar
• Sethi S, Evans N, Grant BJB, et al. New strains of bacteria and exacerbations of chronic obstructive pulmonary disease. N Engl J Med. 2002;347(7):465–471.
   PubMed Web of Science ®Google Scholar
• Sethi S, Murphy TF. Infection in the pathogenesis and course of chronic obstructive pulmonary disease. N Engl J Med. 2008;359(22):2355–2365.
   PubMed Web of Science ®Google Scholar
• Schacker T. The role of secondary lymphatic tissue in immune deficiency of HIV infection. Aids. 2008;22(Suppl 3):S13–S18.
   PubMedGoogle Scholar
• Shipley TW, Kling HM, Morris A, et al. Persistent pneumocystis colonization leads to the development of chronic obstructive pulmonary disease in a nonhuman primate model of AIDS. J Infect Dis. 2010;202(2):302–312.
   PubMed Web of Science ®Google Scholar
• Marsland BJ, Trompette A, Gollwitzer ES. The gut-lung axis in respiratory disease. Ann Am Thorac Soc. 2015;12(Suppl 2):S150–S156.
   PubMed Web of Science ®Google Scholar
• Beck JM. ABCs of the lung microbiome. Ann Am Thorac Soc. 2014;11(Suppl 1):S3–S6.
   PubMedGoogle Scholar
• Bassis CM, Erb-Downward JR, Dickson RP, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6(2):e00037.
   PubMed Web of Science ®Google Scholar
• Dickson RP, Erb-Downward JR, Freeman CM, et al. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann Am Thorac Soc. 2015;12(6):821–830.
   PubMed Web of Science ®Google Scholar
• Willner D, Haynes MR, Furlan M, et al. Spatial distribution of microbial communities in the cystic fibrosis lung. Isme J. 2012;6(2):471–474.
   PubMed Web of Science ®Google Scholar
• Huang YJ, Sethi S, Murphy T, et al. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014;52(8):2813–2823.
   PubMed Web of Science ®Google Scholar
• Price KE, Hampton TH, Gifford AH, et al. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome. 2013;1(1):27.
   PubMed Web of Science ®Google Scholar
• Stressmann FA, Rogers GB, Marsh P, et al. Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation? J Cyst Fibros. 2011;10(5):357–365.
   PubMed Web of Science ®Google Scholar
• Cox MJ, Allgaier M, Taylor B, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010;5(6):e11044.
   PubMed Web of Science ®Google Scholar
• Zhao J, Schloss PD, Kalikin LM, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. 2012;109(15):5809–5814.
   PubMed Web of Science ®Google Scholar
• Li Y, Saxena D, Chen Z, et al. HIV infection and microbial diversity in saliva. J Clin Microbiol. 2014;52(5):1400–1411.
   PubMed Web of Science ®Google Scholar
• Dang AT, Cotton S, Sankaran-Walters S, et al. Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients. BMC Microbiol. 2012;12:153.
   PubMed Web of Science ®Google Scholar
• Vujkovic-Cvijin I, Dunham RM, Iwai S, et al. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013;5(193):193ra91.
   PubMed Web of Science ®Google Scholar
• Mutlu EA, Keshavarzian A, Losurdo J, et al. A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects. PLoS Pathog. 2014;10(2):e1003829.
   PubMed Web of Science ®Google Scholar
• Pérez-Santiago J, Gianella S, Massanella M, et al. Gut Lactobacillales are associated with higher CD4 and less microbial translocation during HIV infection. Aids. 2013;27(12):1921–1931.
   PubMed Web of Science ®Google Scholar
• Monaco CL, Gootenberg DB, Zhao G, et al. Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe. 2016;19(3):311–322.
   PubMed Web of Science ®Google Scholar
• Charlson ES, Bittinger K, Haas AR, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184(8):957–963.
   PubMed Web of Science ®Google Scholar
• Desnues B, Al Moussawi K, Fenollar F. New insights into Whipple’s disease and Tropheryma whipplei infections. Microbes Infect. 2010;12(14–15):1102–1110.
   PubMed Web of Science ®Google Scholar
• Patel SJ, Huard RC, Keller C, et al. Possible case of CNS Whipple’s disease in an adolescent with AIDS. J Int Assoc Physicians AIDS Care (Chic). 2008;7(2):69–73.
   PubMedGoogle Scholar
• Segal LN, Alekseyenko AV, Clemente JC, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1(1):19.
   PubMed Web of Science ®Google Scholar
• Benito N, Moreno A, Miro JM, et al. Pulmonary infections in HIV-infected patients: an update in the 21st century. Eur Respir J. 2012;39(3):730–745.
   PubMed Web of Science ®Google Scholar
• Iwai S, Fei M, Huang D, et al. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol. 2012;50(9):2995–3002.
   PubMed Web of Science ®Google Scholar
• Iwai S, Huang D, Fong 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(4):e95726.
   PubMed Web of Science ®Google Scholar
• Rogers GB, Zain NMM, Bruce KD, et al. A novel microbiota stratification system predicts future exacerbations in bronchiectasis. Ann Am Thorac Soc. 2014;11(4):496–503.
   PubMedGoogle Scholar
• Meynard JL, Barbut F, Guiguet M, et al. Pseudomonas aeruginosa infection in human immunodeficiency virus infected patients. J Infect. 1999;38(3):176–181.
   PubMed Web of Science ®Google Scholar
• Lawley TD, Clare S, Walker AW, et al. Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun. 2009;77(9):3661–3669.
   PubMed Web of Science ®Google Scholar
• Dong Y, Manfredini F, Dimopoulos G, et al. Implication of the mosquito midgut microbiota in the defense against malaria parasites. PLoS Pathog. 2009;5(5):e1000423.
   PubMed Web of Science ®Google Scholar
• Nagano Y, Itoh K, Honda K. The induction of Treg cells by gut-indigenous Clostridium. Curr Opin Immunol. 2012;24(4):392–397.
   PubMed Web of Science ®Google Scholar
• Abreu NA, Nagalingam NA, Song Y, et al. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med. 2012;4(151):151ra124.
   PubMed Web of Science ®Google Scholar
• Atarashi K, Tanoue T, Oshima K, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500(7461):232–236.
   PubMed Web of Science ®Google Scholar
• Atarashi K, Tanoue T, Shima T, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331(6015):337–341.
   PubMed Web of Science ®Google Scholar
• Aslami H, Pulskens WP, Kuipers MT, et al. Hydrogen sulfide donor NaHS reduces organ injury in a rat model of pneumococcal pneumosepsis, associated with improved bio-energetic status. PLoS One. 2013;8(5):e63497.
   PubMed Web of Science ®Google Scholar
• Stressmann FA, Rogers GB, Klem ER, 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(1):281–291.
   PubMed Web of Science ®Google Scholar
• Lim MY, Yoon HS, Rho M, et al. Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans. Sci Rep. 2016;6:23745.
   PubMed Web of Science ®Google Scholar
• Goodrich JK, Waters JL, Poole AC, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789–799.
   PubMed Web of Science ®Google Scholar
• Allais L, Kerckhof F-M, Verschuere S, et al. Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut. Environ Microbiol. 2016;18(5):1352–1363.
   PubMed Web of Science ®Google Scholar
• Biedermann L, Zeitz J, Mwinyi J, et al. Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans. PLoS One. 2013;8(3):e59260.
   PubMed Web of Science ®Google Scholar
• Charlson ES, Chen J, Custers-Allen R, et al. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One. 2010;5(12):e15216.
   PubMed Web of Science ®Google Scholar
• Lee J, Taneja V, Vassallo R. Cigarette smoking and inflammation: cellular and molecular mechanisms. J Dent Res. 2012;91(2):142–149.
   PubMed Web of Science ®Google Scholar
• Morris A, Kingsley LA, Groner G, et al. Prevalence and clinical predictors of Pneumocystis colonization among HIV-infected men. Aids. 2004;18(5):793–798.
   PubMed Web of Science ®Google Scholar
• Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med. 2013;5(7):63.
   PubMed Web of Science ®Google Scholar
• Nguyen LDN, Viscogliosi E, Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol. 2015;6:89.
   PubMed Web of Science ®Google Scholar
• Delhaes L, Monchy S, Fréalle E, et al. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community–implications for therapeutic management. PLoS One. 2012;7(4):e36313.
   PubMed Web of Science ®Google Scholar
• Cui L, Lucht L, Tipton L, et al. Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease. Am J Respir Crit Care Med. 2015;191(8):932–942.
   PubMed Web of Science ®Google Scholar
• Morris A, Alexander T, Radhi S, et al. Airway obstruction is increased in pneumocystis-colonized human immunodeficiency virus-infected outpatients. J Clin Microbiol. 2009;47(11):3773–3776.
   PubMed Web of Science ®Google Scholar
• Morris A, Sciurba FC, Lebedeva IP, et al. Association of chronic obstructive pulmonary disease severity and pneumocystis colonization. Am J Respir Crit Care Med. 2004;170(4):408–413.
   PubMed Web of Science ®Google Scholar
• Christensen PJ, Preston AM, Ling T, et al. 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(8):3481–3490.
   PubMed Web of Science ®Google Scholar
• Hogg JC. Role of latent viral infections in chronic obstructive pulmonary disease and asthma. Am J Respir Crit Care Med. 2001;164(10 Pt 2):S71–S75.
   PubMed Web of Science ®Google Scholar
• Willner D, Furlan M, Haynes M, et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One. 2009;4(10):e7370.
   PubMed Web of Science ®Google Scholar
• Lynch SV. Viruses and microbiome alterations. Ann Am Thorac Soc. 2014;11(Suppl 1):S57–S60.
   PubMedGoogle Scholar
• Scheiblauer H, Reinacher M, Tashiro M, et al. Interactions between bacteria and influenza A virus in the development of influenza pneumonia. J Infect Dis. 1992;166(4):783–791.
   PubMed Web of Science ®Google Scholar
• Tashiro M, Ciborowski P, Klenk HD, et al. Role of staphylococcus protease in the development of influenza pneumonia. Nature. 1987;325(6104):536–537.
   PubMed Web of Science ®Google Scholar
• Jones DP, Park Y, Ziegler TR. Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr. 2012;32:183–202.
   PubMed Web of Science ®Google Scholar
• McHardy IH, Goudarzi M, Tong M, et al. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome. 2013;1(1):17.
   PubMed Web of Science ®Google Scholar
• Vulevic J, Juric A, Walton GE, et al. Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons. Br J Nutr. 2015;114(4):586–595.
   PubMed Web of Science ®Google Scholar
• Cribbs, SK, Park Y, Guidot DM. et al. Metabolomics of bronchoalveolar lavage differentiate healthy HIV-1-infected subjects from controls. AIDS Res Hum Retroviruses. 2014;30(6):579–585.
   PubMed Web of Science ®Google Scholar
• Cribbs, SK, Uppal K, Li S. et al. Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection. Microbiome. 2016;4(1):3.
   PubMed Web of Science ®Google Scholar
• Jones DP. Radical-free biology of oxidative stress. Am J Physiol Cell Physiol. 2008;295(4):C849–C868.
   PubMed Web of Science ®Google Scholar
• Dröge W, Eck HP, Gmünder H, et al. Modulation of lymphocyte functions and immune responses by cysteine and cysteine derivatives. Am J Med. 1991;91(3C):140S–144S.
   PubMedGoogle Scholar
• Dröge W, Eck HP, Gmünder H, et al. Dysregulation of plasma amino acid levels in HIV-infection and cancer and its relevance for the immune system. Amino Acids. 1991;1(2):193–198.
   PubMedGoogle Scholar
• Coaccioli S, Crapa G, Fantera M, et al. Oxidant/antioxidant status in patients with chronic HIV infection. Clin Ter. 2010;161(1):55–58.
   PubMed Web of Science ®Google Scholar
• Cribbs SK, Guidot DM, Martin GS, et al. Anti-retroviral therapy is associated with decreased alveolar glutathione levels even in healthy HIV-infected individuals. PLoS One. 2014;9(2):e88630.
   PubMed Web of Science ®Google Scholar
• Lassiter C, Fan X, Joshi PC, et al. HIV-1 transgene expression in rats causes oxidant stress and alveolar epithelial barrier dysfunction. AIDS Res Ther. 2009;6:1.
   PubMedGoogle Scholar
• Dröge W, Eck HP, Mihm S. HIV-induced cysteine deficiency and T-cell dysfunction–a rationale for treatment with N-acetylcysteine. Immunol Today. 1992;13(6):211–214.
   PubMedGoogle Scholar
• Kinscherf R, Fischbach T, Mihm S, et al. Effect of glutathione depletion and oral N-acetyl-cysteine treatment on CD4+ and CD8+ cells. Faseb J. 1994;8(6):448–451.
   PubMed Web of Science ®Google Scholar
• Ubhi BK, Cheng KK, Dong J, et al. Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with COPD. Mol Biosyst. 2012;8(12):3125–3133.
   PubMed Web of Science ®Google Scholar
• Nobakht MGBF, Aliannejad R, Rezaei-Tavirani M, et al. The metabolomics of airway diseases, including COPD, asthma and cystic fibrosis. Biomarkers. 2015;20(1):5–16.
   PubMed Web of Science ®Google Scholar