The Microbiome in Cystic Fibrosis

Clinics in Chest Medicine

Volumn 37, Issue 1, 2016, Pages 59-67

  Huang, Yvonne J ^a   LiPuma, John J ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Bacteria; Culture independent; Fungi; Gut; Lung; Microbiota; Virus

Indexed keywords

BACTERIAL COLONIZATION; BACTERIUM CULTURE; BRONCHIECTASIS; CLINICAL FEATURE; CYSTIC FIBROSIS; DISEASE EXACERBATION; FUNGAL COMMUNITY; FUNGUS CULTURE; GASTROINTESTINAL TRACT; HUMAN; INTESTINE FLORA; LUNG INFECTION; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; MICROBIOME; MOLECULAR GENETICS; MORBIDITY; NONHUMAN; PATHOPHYSIOLOGY; PRIORITY JOURNAL; RESPIRATORY SYSTEM; REVIEW; RNA VIRUS INFECTION; SEQUENCE ANALYSIS; SPUTUM CULTURE; TRANSCRIPTOMICS; VIRUS CULTURE; BACTERIAL INFECTION; COMPLICATION; LUNG; MICROBIOLOGY; MICROFLORA;

BACTERIAL INFECTIONS; CYSTIC FIBROSIS; HUMANS; LUNG; MICROBIOTA;

EID: 84959318214     PISSN: 02725231     EISSN: 15578216     Source Type: Journal    
DOI: 10.1016/j.ccm.2015.10.003     Document Type: Review

References (73)

1. Harris J.K., De Groote M.A., Sagel S.D., et al. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 2007, 104(51):20529-20533.
2. Tunney M.M., Field T.R., Moriarty T.F., et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 2008, 177:995-1001.
3. Cox M.J., Allgaier M., Taylor B., et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 2010, 5(6):e11044.
4. Klepac-Ceraj V., Lemon K.P., Martin T.R., et al. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol 2010, 12:1293-1303.
5. van der Gast C.J., Walker A.W., Stressmann F.A., et al. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J 2011, 5(5):780-791.
6. Fodor A.A., Klem E.R., Gilpin D.F., et al. 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(9):e45001.
7. Zhao J., Schloss P.D., Kalikin L.M., et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 2012, 109(15):5809-5814.
8. Carmody L.A., Zhao J., Kalikin L.M., et al. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome 2015, 3:12.
9. Price K.E., Hampton T.H., Gifford A.H., et al. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome 2013, 1(1):27.
10. Zemanick E.T., Harris J.K., Wagner B.D., et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013, 8(4):e62917.
11. Renwick J., McNally P., John B., et al. The microbial community of the cystic fibrosis airway is disrupted in early life. PLoS One 2014, 9(12):e109798.
12. Coburn B., Wang P.W., Diaz Caballero J., et al. Lung microbiota across age and disease stage in cystic fibrosis. Sci Rep 2015, 5:10241.
13. 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.
14. Willger S.D., Grim S.L., Dolben E.L., et al. Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis. Microbiome 2014, 2:40.
15. Mounier J., Gouëllo A., Keravec M., et al. Use of denaturing high-performance liquid chromatography (DHPLC) to characterize the bacterial and fungal airway microbiota of cystic fibrosis patients. J Microbiol 2014, 52(4):307-314.
16. 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.
17. Duytschaever G., Huys G., Bekaert M., et al. Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings. Appl Environ Microbiol 2011, 77(22):8015-8024.
18. Duytschaever G., Huys G., Bekaert M., et al. Dysbiosis of bifidobacteria and Clostridium cluster XIVa in the cystic fibrosis fecal microbiota. J Cyst Fibros 2013, 12(3):206-215.
19. Madan J.C., Koestler D.C., Stanton B.A., 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). [pii:e00251-12].
20. Hoen A.G., Li J., Moulton L.A., et al. Associations between gut microbial colonization in early life and respiratory outcomes in cystic fibrosis. J Pediatr 2015, 167(1):138-147.e1-3.
21. Gelfond D., Borowitz D. Gastrointestinal complications of cystic fibrosis. Clin Gastroenterol Hepatol 2013, 11(4):333-342. [quiz: e30-1].
22. Han M.K., Huang Y.J., Lipuma J.J., et al. Significance of the microbiome in obstructive lung disease. Thorax 2012, 67(5):456-463.
23. Huang Y.J., Charlson E.S., Collman R.G., 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):1382-1387.
24. Dickson R.P., Erb-Downward J.R., Huffnagle G.B. The role of the bacterial microbiome in lung disease. Expert Rev Respir Med 2013, 7(3):245-257.
25. Morris A., Beck J.M., Schloss P.D., et al. Lung HIV microbiome project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013, 187(10):1067-1075.
26. Brown P.S., Pope C.E., Marsh R.L., et al. Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota. Ann Am Thorac Soc 2014, 11(7):1049-1055.
27. Zemanick E.T., Wagner B.D., Robertson C.E., et al. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc 2015, 12(2):221-229.
28. Boutin S., Graeber S.Y., Weitnauer M., et al. Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLoS One 2015, 10(1):e0116029.
29. Venkataraman A., Bassis C.M., Beck J.M., et al. Application of a neutral community model to assess structuring of the human lung microbiome. MBio 2015, 6(1). [pii:e02284-14].
30. Dickson R.P., Erb-Downward J.R., Huffnagle G.B. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med 2014, 2(3):238-246.
31. Willner D., Haynes M.R., Furlan M., et al. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J 2012, 6(2):471-474.
32. Gilligan P.H. Infections in patients with cystic fibrosis: diagnostic microbiology update. Clin Lab Med 2014, 34(2):197-217. [Review].
33. Dasenbrook E.C., Checkley W., Merlo C.A., et al. Association between respiratory tract methicillin-resistant Staphylococcus aureus and survival in cystic fibrosis. JAMA 2010, 303(23):2386-2392.
34. Martiniano S.L., Nick J.A. Nontuberculous mycobacterial infections in cystic fibrosis. Clin Chest Med 2015, 36(1):101-115. [Review].
35. Wolter D.J., Emerson J.C., McNamara S., et al. Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis. Clin Infect Dis 2013, 57(3):384-391.
36. Muhlebach M.S., Heltshe S.L., Popowitch E.B., The STAR-CF Study Team, et al. Multicenter observational study on factors and outcomes associated with different MRSA types in children with cystic fibrosis. Ann Am Thorac Soc 2015, 12(6):864-871.
37. Cogen J., Emerson J., Sanders D.B., EPIC Study Group, et al. Risk factors for lung function decline in a large cohort of young cystic fibrosis patients. Pediatr Pulmonol 2015, 50(8):763-770.
38. Parkins M.D., Floto R.A. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros 2015, 14(3):293-304.
39. De Baets F., Schelstraete P., Van Daele S., et al. Achromobacter xylosoxidans in cystic fibrosis: prevalence and clinical relevance. J Cyst Fibros 2007, 6(1):75-78.
40. Lambiase A., Catania M.R., Del Pezzo M., et al. Achromobacter xylosoxidans respiratory tract infection in cystic fibrosis patients. Eur J Clin Microbiol Infect Dis 2011, 30(8):973-980.
41. Marzuillo C., De Giusti M., Tufi D., et al. Molecular characterization of Stenotrophomonas maltophilia isolates from cystic fibrosis patients and the hospital environment. Infect Control Hosp Epidemiol 2009, 30(8):753-758.
42. Tunney M.M., Klem E.R., Fodor A.A., et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011, 66:579-584.
43. Twomey K.B., Alston M., An S.Q., et al. Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation. PLoS One 2013, 8(12):e82432.
44. Chmiel J.F., Aksamit T.R., Chotirmall S.H., et al. Antibiotic management of lung infections in cystic fibrosis. II. Nontuberculous mycobacteria, anaerobic bacteria, and fungi. Ann Am Thorac Soc 2014, 11(8):1298-1306.
45. Jones A.M. Anaerobic bacteria in cystic fibrosis: pathogens or harmless commensals?. Thorax 2011, 66(7):558-559.
46. Field T.R., Sibley C.D., Parkins M.D., et al. The genus Prevotella in cystic fibrosis airways. Anaerobe 2010, 16(4):337-344.
47. Duan K., Dammel C., Stein J., et al. Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol Microbiol 2003, 50(5):1477-1491.
48. Ghorbani P., Santhakumar P., Hu Q., et al. Short-chain fatty acids affect cystic fibrosis airway inflammation and bacterial growth. Eur Respir J 2015, 46(4):1033-1045.
49. Ramsey K.A., Ranganathan S., Park J., et al. Early respiratory infection is associated with reduced spirometry in children with cystic fibrosis. Am J Respir Crit Care Med 2014, 190(10):1111-1116.
50. Wielpütz M.O., Puderbach M., Kopp-Schneider A., et al. Magnetic resonance imaging detects changes in structure and perfusion, and response to therapy in early cystic fibrosis lung disease. Am J Respir Crit Care Med 2014, 189(8):956-965.
51. Carmody L.A., Zhao J., Schloss P.D., et al. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc 2013, 10(3):179-187.
52. Cui L., Morris A., Ghedin E. The human mycobiome in health and disease. Genome Med 2013, 5(7):63. [Review].
53. Nguyen L.D., Viscogliosi E., Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol 2015, 6:89. [Review].
54. Kramer R., Sauer-Heilborn A., Welte T., et al. A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements. J Clin Microbiol 2015, 53(9):2900-2907.
55. Nagano Y., Elborn J.S., Millar B.C., et al. Comparison of techniques to examine the diversity of fungi in adult patients with cystic fibrosis. Med Mycol 2010, 48:166-176.
56. Goffard A., Lambert V., Salleron J., et al. Virus and cystic fibrosis: rhinoviruses are associated with exacerbations in adult patients. J Clin Virol 2014, 60(2):147-153.
57. Esther C.R., Lin F.C., Kerr A., et al. Respiratory viruses are associated with common respiratory pathogens in cystic fibrosis. Pediatr Pulmonol 2014, 49(9):926-931.
58. Flight W.G., Bright-Thomas R.J., Tilston P., et al. Incidence and clinical impact of respiratory viruses in adults with cystic fibrosis. Thorax 2014, 69(3):247-253.
59. Asner S., Waters V., Solomon M., et al. Role of respiratory viruses in pulmonary exacerbations in children with cystic fibrosis. J Cyst Fibros 2012, 11(5):433-439.
60. Wylie K.M., Weinstock G.M., Storch G.A. Emerging view of the human virome. Transl Res 2012, 160(4):283-290. [Review].
61. Lim Y.W., Schmieder R., Haynes M., et al. Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros 2013, 12(2):154-164.
62. James C.E., Davies E.V., Fothergill J.L., et al. Lytic activity by temperate phages of Pseudomonas aeruginosa in long-term cystic fibrosis chronic lung infections. ISME J 2015, 9(6):1391-1398.
63. Saussereau E., Vachier I., Chiron R., et al. Effectiveness of bacteriophages in the sputum of cystic fibrosis patients. Clin Microbiol Infect 2014, 20(12):O983-O990.
64. Barr J.J., Auro R., Furlan M., et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 2013, 110:10771-10776.
65. Kamal F., Dennis J.J. Burkholderia cepacia complex phage-antibiotic synergy (PAS): antibiotics stimulate lytic phage activity. Appl Environ Microbiol 2015, 81(3):1132-1138.
66. Smillie C.S., Smith M.B., Friedman J., et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 2011, 480:241-244.
67. Langille M.G., Zaneveld J., Caporaso J.G., et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013, 31(9):814-821.
68. Quinn R.A., Lim Y.W., Maughan H., et al. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. MBio 2014, 5(2):e00956-13.
69. Quinn R.A., Whiteson K., Lim Y.W., et al. Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. ISME J 2015, 9(4):1024-1038. [Erratum appears in ISME J 2015;9(4):1052].
70. Saavedra J.M., Dattilo A.M. Early development of intestinal microbiota: implications for future health. Gastroenterol Clin North Am 2012, 41(4):717-731.
71. Bäckhed F., Roswall J., Peng Y., et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 2015, 17(5):690-703.
72. del Campo R., Garriga M., Pérez-Aragón A., et al. Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: a double blind prospective study. J Cyst Fibros 2014, 13(6):716-722.
73. Bruzzese E., Callegari M.L., Raia V., et al. Disrupted intestinal microbiota and intestinal inflammation in children with cystic fibrosis and its restoration with Lactobacillus GG: a randomised clinical trial. PLoS One 2014, 9(2):e87796.