'The Microbiome and the Pathophysiology of Asthma'

Respiratory Research

Volumn 17, Issue 1, 2016, Pages

  Sullivan, Ashley ^b   Hunt, Eoin ^a,c   MacSharry, John ^b,c   Murphy, Desmond M ^a,c  

^a University College Cork and INFANT Centre   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Asthma; Epithelium; Host; Hygiene hypothesis; Inflammation; Medicine; Microbe dialogue; Microbiology; Translational research

Indexed keywords

ANTIASTHMATIC AGENT; ANTIBIOTIC AGENT; CORTICOSTEROID; AUTACOID;

ASTHMA; CLINICAL RESEARCH; DNA SEQUENCE; FUNGUS; HUMAN; LUNG ALVEOLUS EPITHELIUM; MICROBIOME; NONHUMAN; PATHOPHYSIOLOGY; REVIEW; SEQUENCE ANALYSIS; VIRUS; ANIMAL; BACTERIAL LOAD; HOST PATHOGEN INTERACTION; HYGIENE HYPOTHESIS; LUNG; METABOLISM; MICROBIOLOGY; MICROFLORA; RISK FACTOR; SIGNAL TRANSDUCTION; VIROLOGY; VIRUS LOAD;

ANIMALS; ASTHMA; BACTERIAL LOAD; HOST-PATHOGEN INTERACTIONS; HUMANS; HYGIENE HYPOTHESIS; INFLAMMATION MEDIATORS; LUNG; MICROBIOTA; RISK FACTORS; SIGNAL TRANSDUCTION; VIRAL LOAD;

EID: 85000461293     PISSN: 14659921     EISSN: 1465993X     Source Type: Journal    
DOI: 10.1186/s12931-016-0479-4     Document Type: Review

References (101)

1. Kim HY, DeKruyff RH, Umetsu DT. The many paths to asthma: phenotype shaped by innate and adaptive immunity. Nat Immunol. 2010;11(7):577-84.
2. Hilty M, et al. Disordered microbial communities in asthmatic airways. PLoS One. 2010;5:1.
3. Edwards MR, et al. The microbiology of asthma. Nat Rev Micro. 2012;10(7):459-71.
4. Burney P, Jarvis D, Perez-Padilla R. The global burden of chronic respiratory disease in adults. Int J Tuberc Lung Dis. 2015;19(1):10-20.
5. Umetsu DT, et al. Asthma: an epidemic of dysregulated immunity. Nat Immunol. 2002;3(8):715-20.
6. Noverr MC, Huffnagle GB. Does the microbiota regulate immune responses outside the gut? Trends Microbiol. 2004;12(12):562-8.
7. Marsland BJ. Influences of the Microbiome on the Early Origins of Allergic Asthma. Ann Am Thorac Soc. 2013;10:S165-9.
8. Holgate ST, Polosa R. Treatment strategies for allergy and asthma. Nat Rev Immunol. 2008;8(3):218-30.
9. Aho VT, et al. The microbiome of the human lower airways: a next generation sequencing perspective. World Allergy Organ J. 2015;8(1):23.
10. Marsland BJ, Gollwitzer ES. Host-microorganism interactions in lung diseases. Nat Rev Immunol. 2014;14(12):827-35.
11. Segal LN, Blaser MJ. A brave new world: the lung microbiota in an era of change. Ann Am Thorac Soc. 2014;11 Suppl 1:S21-7.
12. Huffnagle GB, Dickson RP. The bacterial micro biota in inflammatory lung diseases. Clin Immunol. 2015;159(2):177-82.
13. Erb-Downward JR, et al. Analysis of the Lung Microbiome in the "Healthy" Smoker and in COPD. PLoS One. 2011;6(2), e16384.
14. Turnbaugh PJ, et al. The Human Microbiome Project. Nature. 2007;449(7164):804-10.
15. Segal LN, Rom WN, Weiden MD. Lung microbiome for clinicians. New discoveries about bugs in healthy and diseased lungs. Ann Am Thorac Soc. 2014;11(1):108-16.
16. Charlson ES, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184(8):957-63.
17. Segal LN, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1(1):19.
18. Salami O, Marsland BJ. Has the airway microbiome been overlooked in respiratory disease? Genome Med. 2015;7(1):62.
19. Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014;2(3):238-46.
20. Dickson RP, 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):821-30.
21. Venkataraman A, et al. Application of a neutral community model to assess structuring of the human lung microbiome. MBio. 2015;6:1.
22. Bassis CM, 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.
23. Madan JC, et al. Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. MBio. 2012;3:4.
24. Huang YJ, et al. 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(12):1382-7.
25. Boyton RJ, et al. Immune mechanisms and the impact of the disrupted lung microbiome in chronic bacterial lung infection and bronchiectasis. Clin Exp Immunol. 2013;171(2):117-23.
26. Ooi CY, Durie PR. Cystic fibrosis from the gastroenterologist's perspective. Nat Rev Gastroenterol Hepatol. 2016;13(3):175-85.
27. Al-Momani H, et al. Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients. Sci Rep. 2016;6:26985.
28. Reen FJ, et al. Bile signalling promotes chronic respiratory infections and antibiotic tolerance. Sci Rep. 2016;6:29768.
29. Sze MA, Hogg JC, Sin DD. Bacterial microbiome of lungs in COPD. Int J Chron Obstruct Pulmon Dis. 2014;9:229-38.
30. Morris A, Gibson K, Collman RG. The Lung Microbiome in Idiopathic Pulmonary Fibrosis. What Does It Mean and What Should We Do about It? Am J Respir Crit Care Med. 2014;190(8):850-2.
31. Hammad H, Lambrecht BN. Dendritic cells and epithelial cells: linking innate and adaptive immunity in asthma. Nat Rev Immunol. 2008;8(3):193-204.
32. Levy ML, et al. International Primary Care Respiratory Group (IPCRG) Guidelines: Diagnosis of respiratory diseases in primary care. Prim Care Respir J. 2006;15:20.
33. Murphy DM, O'Byrne PM. Recent advances in the pathophysiology of asthma. Chest. 2010;137(6):1417-26.
34. Lambrecht BN, Hammad H. The airway epithelium in asthma. Nat Med. 2012;18(5):684-92.
35. Dickson RP, Martinez FJ, Huffnagle GB. The role of the microbiome in exacerbations of chronic lung diseases. Lancet. 2014;384(9944):691-702.
36. Sanders DB, et al. Return of FEV1 after pulmonary exacerbation in children with cystic fibrosis. Pediatr Pulmonol. 2010;45(2):127-34.
37. Bateman ED, et al. Global strategy for asthma management and prevention: GINA executive summary. Eur Respir J. 2008;31(1):143-78.
38. Holt PG, et al. The role of allergy in the development of asthma. Nature. 1999;402:B12-7.
39. Joyce SA, et al. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci U S A. 2014;111(20):7421-6.
40. Liang X, Bushman FD, FitzGerald GA. Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock. Proc Natl Acad Sci U S A. 2015;112(33):10479-84.
41. Gibbs J, et al. An epithelial circadian clock controls pulmonary inflammation and glucocorticoid action. Nat Med. 2014;20(8):919-26.
42. Cash HL, et al. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science. 2006;313(5790):1126-30.
43. Sonnenberg Gregory F, Artis D. Innate Lymphoid Cell Interactions with Microbiota: Implications for Intestinal Health and Disease. Immunity. 2012;37(4):601-10.
44. Ruane D, et al. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses. J Exp Med. 2016;213(1):53-73.
45. Fujimura KE, Lynch SV. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe. 2015;17(5):592-602.
46. O'Neill LAJ, Bowie AG. The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling. Nat Rev Immunol. 2007;7(5):353-64.
47. Bassetti S, et al. Dispersal of Staphylococcus aureus Into the Air Associated With a Rhinovirus Infection. Infect Control Hosp Epidemiol. 2005;26(2):196-203.
48. Bossios A, et al. Rhinovirus infection induces cytotoxicity and delays wound healing in bronchial epithelial cells. Respir Res. 2005;6(1):114-4.
49. Message SD, et al. Rhinovirus-induced lower respiratory illness is increased in asthma and related to virus load and Th1/2 cytokine and IL-10 production. Proc Natl Acad Sci U S A. 2008;105(36):13562-7.
50. Bisgaard H, et al. Childhood Asthma after Bacterial Colonization of the Airway in Neonates. N Engl J Med. 2007;357(15):1487-95.
51. Bisgaard H, et al. Association of bacteria and viruses with wheezy episodes in young children: prospective birth cohort study. BMJ: Br Med J. 2010;341(7776):770-0.
52. Lambrecht BN, Hammad H. The role of dendritic and epithelial cells as master regulators of allergic airway inflammation. Lancet. 2010;376(9743):835-43.
53. Marsland BJ, Salami O. Microbiome influences on allergy in mice and humans. Curr Opin Immunol. 2015;36:94-100.
54. Dominguez-Bello MG, Blaser MJ. Asthma: Undoing millions of years of coevolution in early life? Sci Transl Med. 2015;307:307fs39-9.
55. Thavagnanam S, et al. A meta-analysis of the association between Caesarean section and childhood asthma. Clin Exp Allergy. 2008;38(4):629-33.
56. Murk W, Risnes KR, Bracken MB. Prenatal or early-life exposure to antibiotics and risk of childhood asthma: a systematic review. Pediatrics. 2011;127(6):1125-38.
57. Ege MJ, et al. Exposure to Environmental Microorganisms and Childhood Asthma. N Engl J Med. 2011;364(8):701-9.
58. Schuijs MJ, et al. Farm dust and endotoxin protect against allergy through A20 induction in lung epithelial cells. Science. 2015;349(6252):1106-10.
59. Braun-Fahrlander C, et al. Environmental exposure to endotoxin and its relation to asthma in school-age children. N Engl J Med. 2002;347(12):869-77.
60. Van Strien RT, et al. Microbial exposure of rural school children, as assessed by levels of N-acetyl-muramic acid in mattress dust, and its association with respiratory health. J Allergy Clin Immunol. 2004;113(5):860-7.
61. Arrieta MC, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7:307.
62. Pattaroni C, Marsland BJ. Asthma Prevention: Right Bugs, Right Time? Cell Host Microbe. 2015;18(5):523-5.
63. Trompette A, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20(2):159-66.
64. Olszak T, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336(6080):489-93.
65. Marsland BJ, Yadava K, Nicod LP. The airway microbiome and disease. Chest. 2013;144(2):632-7.
66. Forsythe P, Inman MD, Bienenstock J. Oral treatment with live Lactobacillus reuteri inhibits the allergic airway response in mice. Am J Respir Crit Care Med. 2007;175(6):561-9.
67. Karimi K, et al. Lactobacillus reuteri-induced regulatory T cells protect against an allergic airway response in mice. Am J Respir Crit Care Med. 2009;179(3):186-93.
68. Nembrini C, et al. Bacterial-induced protection against allergic inflammation through a multicomponent immunoregulatory mechanism. Thorax. 2011;66(9):755-63.
69. MacSharry J, et al. Immunomodulatory effects of feeding with Bifidobacterium longum on allergen-induced lung inflammation in the mouse. Pulm Pharmacol Ther. 2012;25(4):325-34.
70. Russell SL, et al. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 2012;13(5):440-7.
71. Russell SL, et al. Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases. J Allergy Clin Immunol. 2015;135(1):100-9.
72. Chen Y, Blaser MJ. Inverse associations of Helicobacter pylori with asthma and allergy. Arch Intern Med. 2007;167(8):821-7.
73. Banatvala N, et al. The cohort effect and Helicobacter pylori. J Infect Dis. 1993;168(1):219-21.
74. Blaser MJ, Chen Y, Reibman J. Does Helicobacter pylori protect against asthma and allergy? Gut. 2008;57(5):561-7.
75. Charlson ES, et al. Assessing Bacterial Populations in the Lung by Replicate Analysis of Samples from the Upper and Lower Respiratory Tracts. PLoS One. 2012;7:9.
76. Marri PR, et al. Asthma-associated differences in microbial composition of induced sputum. J Allergy Clin Immunol. 2013;131(2):346-352.e3.
77. Blaser MJ, Falkow S. What are the consequences of the disappearing human microbiota? Nat Rev Micro. 2009;7(12):887-94.
78. Uehara A, et al. Various human epithelial cells express functional Toll-like receptors, NOD1 and NOD2 to produce anti-microbial peptides, but not proinflammatory cytokines. Mol Immunol. 2007;44(12):3100-11.
79. Gómez MI, Prince A. Airway epithelial cell signaling in response to bacterial pathogens. Pediatr Pulmonol. 2008;43(1):11-9.
80. Suzuki T, Chow C-W, Downey GP. Role of innate immune cells and their products in lung immunopathology. Int J Biochem Cell Biol. 2008;40(6-7):1348-61.
81. Proud D, Leigh R. Epithelial cells and airway diseases. Immunol Rev. 2011;242(1):186-204.
82. Toews GB. Cytokines and the lung. Eur Respir J. 2001;18(34):3s-17s.
83. Mitchell, P.D. and P.M. O'Byrne, Biologics and the lung: TSLP and other epithelial cell-derived cytokines in asthma. Pharmacology & Therapeutics. 2007. doi: 10.1016/j.pharmthera.2016.06.009.
84. Denning DW, et al. The link between fungi and severe asthma: a summary of the evidence. Eur Respir J. 2006;27(3):615-26.
85. Lambrecht BN, Hammad H. Dendritic Cell and Epithelial Cell Interactions at the Origin of Murine Asthma. Ann Am Thorac Soc. 2014;11(5):S236-43.
86. Byrne AJ, Maher TM, Lloyd CM. Pulmonary Macrophages: A New Therapeutic Pathway in Fibrosing Lung Disease? Trends Mol Med. 2016;22(4):303-16.
87. Berg RD, et al. Lysosomal Disorders Drive Susceptibility to Tuberculosis by Compromising Macrophage Migration. Cell. 2016;165(1):139-52.
88. Busse WW, Lemanske Jr RF, Gern JE. Role of viral respiratory infections in asthma and asthma exacerbations. Lancet. 2010;376(9743):826-34.
89. Sigurs N, et al. Respiratory syncytial virus bronchiolitis in infancy is an important risk factor for asthma and allergy at age 7. Am J Respir Crit Care Med. 2000;161(5):1501-7.
90. Hament JM, et al. Enhanced adherence of Streptococcus pneumoniae to human epithelial cells infected with respiratory syncytial virus. Pediatr Res. 2004;55(6):972-8.
91. Jackson DJ, et al. Wheezing rhinovirus illnesses in early life predict asthma development in high-risk children. Am J Respir Crit Care Med. 2008;178(7):667-72.
92. Hansel TT, Johnston SL, Openshaw PJ. Microbes and mucosal immune responses in asthma. Lancet. 2013;381(9869):861-73.
93. Beigelman A, Weinstock GM, Bacharier LB. The relationships between environmental bacterial exposure, airway bacterial colonization, and asthma. Curr Opin Allergy Clin Immunol. 2014;14(2):137-42.
94. Ege MJ, et al. Not all farming environments protect against the development of asthma and wheeze in children. J Allergy Clin Immunol. 2007;119(5):1140-7.
95. Van Woerden HC, et al. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infect Dis. 2013;13:69.
96. Wheeler ML, et al. Immunological Consequences of Intestinal Fungal Dysbiosis. Cell Host Microbe. 2016;19(6):865-73.
97. Targonski PV, Persky VW, Ramekrishnan V. Effect of environmental molds on risk of death from asthma during the pollen season. J Allergy Clin Immunol. 1995;95(5 Pt 1):955-61.
98. Black PN, Udy AA, Brodie SM. Sensitivity to fungal allergens is a risk factor for life-threatening asthma. Allergy. 2000;55(5):501-4.
99. O'Driscoll BR, Hopkinson LC, Denning DW. Mold sensitization is common amongst patients with severe asthma requiring multiple hospital admissions. BMC Pulm Med. 2005;5(1):1-10.
100. Herbst T, et al. Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am J Respir Crit Care Med. 2011;184(2):198-205.
101. Thorburn AN, et al. Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun. 2015;6:7320.