The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection

Tuberculosis

Volumn 95, Issue 6, 2015, Pages 651-658

  Adami, Alexander J ^a   Cervantes, Jorge L ^a,b  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^b Division of Pediatric Infectious Diseases   (United States)

Author keywords

Alveolar macrophages; Innate immune; Lung microbiome; Mycobacterium tuberculosis; Phagosome; Pulmonary alveoli

Indexed keywords

POLYPEPTIDE ANTIBIOTIC AGENT; VITAMIN D; TUBERCULOSTATIC AGENT;

ANTIGEN RECOGNITION; BACTERIAL LOAD; COMMUNITY STRUCTURE; DIABETES MELLITUS; DYSBIOSIS; HUMAN; IMMUNE RESPONSE; INNATE IMMUNITY; INTESTINE FLORA; LUNG ALVEOLUS; LUNG ALVEOLUS EPITHELIUM CELL; LUNG TUBERCULOSIS; MICROBIAL COMMUNITY; MICROBIOME; MICROFLORA; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SAMPLING; SPUTUM; COMORBIDITY; DRUG EFFECTS; HOST PATHOGEN INTERACTION; IMMUNOLOGY; LUNG ALVEOLUS MACROPHAGE; MICROBIOLOGY; PATHOGENICITY; RISK FACTOR; TREATMENT OUTCOME; TUBERCULOSIS, PULMONARY; TUMOR MICROENVIRONMENT;

ANTITUBERCULAR AGENTS; CELLULAR MICROENVIRONMENT; COMORBIDITY; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNITY, INNATE; MACROPHAGES, ALVEOLAR; MICROBIOTA; MYCOBACTERIUM TUBERCULOSIS; PULMONARY ALVEOLI; RISK FACTORS; TREATMENT OUTCOME; TUBERCULOSIS, PULMONARY;

EID: 84948719829     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2015.07.004     Document Type: Review

References (144)

1. A. Zumla, M. Raviglione, R. Hafner, and C.F. von Reyn Tuberculosis N Engl J Med 368 8 2013 745 755
2. H.J. Chapman, and M. Lauzardo Advances in diagnosis and treatment of latent tuberculosis infection J Am Board Fam Med 27 5 2014 704 712
3. M.J. Cox, W.O. Cookson, and M.F. Moffatt Sequencing the human microbiome in health and disease Hum Mol Genet 22 R1 2013 R88 R94
4. A.W. Hui, H.W. Lau, T.H. Chan, and S.K. Tsui The human microbiota: a new direction in the investigation of thoracic diseases J Thorac Dis 5 Suppl. 2 2013 S127 S131
5. M.J. Blaser The microbiome revolution J Clin Invest 124 10 2014 4162 4165
6. D.S. Spasova, and C.D. Surh Blowing on embers: commensal microbiota and our immune system Front Immunol 5 2014 318
7. T. Escherich Die darmbakterien des säuglings und ihre beziehungen zur physiologie der verdauung Enterobacteria of infants and their relation to digestion physiology 1886 F. Enke Stuttgart
8. C.A. Herter, and A.I. Kendall The influence of dietary alternations on the types of intestinal flora J Biol Chem 7 3 1910 203 236
9. J.C. Torrey The regulation of the intestinal Flora of Dogs through diet J Med Res 39 3 1919 415 447
10. C.C. Crowe, W.E. Sanders, and S. Longley Bacterial interference. II. Role of the normal throat flora in prevention of colonization by group A Streptococcus J Infect Dis 128 4 1973 527 532
11. Y. Belkaid, and T.W. Hand Role of the microbiota in immunity and Inflammation Cell 157 1 2014 121 141
12. Z. Wang, E. Klipfell, B.J. Bennett, R. Koeth, B.S. Levison, B. Dugar, and et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease Nature 472 7341 2011 57 63
13. R. Diaz Heijtz, S. Wang, F. Anuar, Y. Qian, B. Björkholm, A. Samuelsson, and et al. Normal gut microbiota modulates brain development and behavior Proc Natl Acad Sci USA 108 7 2011 3047 3052
14. D.C. Savage Microbial ecology of the gastrointestinal tract Annu Rev Microbiol 31 1977 107 133
15. F. Bäckhed, R.E. Ley, J.L. Sonnenburg, D.A. Peterson, and J.I. Gordon Host-bacterial mutualism in the human intestine Sci (New York, NY) 307 5717 2005 1915 1920
16. L.N. Segal, and M.J. Blaser A brave new world: the lung microbiota in an era of change Ann American Thorac Soc 11 Suppl. 1 2014 S21 S27
17. R.P. Dickson, J.R. Erb-Downward, and G.B. Huffnagle Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis Lancet Respir Med 2 3 2014 238 246
18. E. Metchnikoff The prolongation of life: optimistic studies (P. C. Mitchell, trans.) 1908 G.P. Putnam's Sons New York & London
19. A. Döderlein Das scheidensekret und seine bedeutung für das puerperalfieber 1892 Besold
20. W.G. Johanson, A.K. Pierce, and J.P. Sanford Changing pharyngeal bacterial flora of hospitalized patients. Emergence of gram-negative bacilli N. Engl J Med 281 21 1969 1137 1140
21. J.H. Higuchi, J.J. Coalson, and W.G. Johanson Bacteriologic diagnosis of nosocomial pneumonia in primates. Usefulness of the protected specimen brush Am Rev Respir Dis 125 1 1982 53 57
22. R.P. Baughman, J.E. Thorpe, J. Staneck, M. Rashkin, and P.T. Frame Use of the protected specimen brush in patients with endotracheal or tracheostomy tubes Chest 91 2 1987 233 236
23. J.E. Thorpe, R.P. Baughman, P.T. Frame, T.A. Wesseler, and J.L. Staneck Bronchoalveolar lavage for diagnosing acute bacterial pneumonia J Infect Dis 155 5 1987 855 861
24. J. Chastre, J.Y. Fagon, P. Soler, M. Bornet, Y. Domart, J.L. Trouillet, and et al. Diagnosis of nosocomial bacterial pneumonia in intubated patients undergoing ventilation: comparison of the usefulness of bronchoalveolar lavage and the protected specimen brush Am J Med 85 4 1988 499 506
25. J. Peterson, S. Garges, M. Giovanni, P. McInnes, L. Wang, J.A. Schloss, and et al. The NIH human microbiome project Genome Res 19 12 2009 2317 2323
26. A. Suau, R. Bonnet, M. Sutren, J.J. Godon, G.R. Gibson, M.D. Collins, and et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut Appl Environ Microbiol 65 11 1999 4799 4807
27. V. Torsvik, J. Goksøyr, and F.L. Daae High diversity in DNA of soil bacteria Appl Environ Microbiol 56 3 1990 782 787
28. M. Hilty, C. Burke, H. Pedro, P. Cardenas, A. Bush, C. Bossley, and et al. Disordered microbial communities in asthmatic airways PLoS One 5 1 2010
29. E.S. Charlson, K. Bittinger, A.R. Haas, A.S. Fitzgerald, I. Frank, A. Yadav, and et al. Topographical continuity of bacterial populations in the healthy human respiratory tract Am J Respir Crit Care Med 184 8 2011 957 963
30. J.R. Erb-Downward, D.L. Thompson, M.K. Han, C.M. Freeman, L. McCloskey, L.A. Schmidt, and et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD PLoS One 6 2 2011
31. Y.J. Huang, C.E. Nelson, E.L. Brodie, T.Z. Desantis, M.S. Baek, J. Liu, and et al. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma J Allergy Clin Immunol 127 2 2011 372 381 e371-373
32. M.A. Sze, P.A. Dimitriu, S. Hayashi, W.M. Elliott, J.E. McDonough, J.V. Gosselink, and et al. The lung tissue microbiome in chronic obstructive pulmonary disease Am J Respir Crit Care Med 185 10 2012 1073 1080
33. E.S. Charlson, K. Bittinger, J. Chen, J.M. Diamond, H. Li, R.G. Collman, and et al. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts PLoS One 7 9 2012
34. A.A. Pragman, H.B. Kim, C.S. Reilly, C. Wendt, and R.E. Isaacson The lung microbiome in moderate and severe chronic obstructive pulmonary disease PLoS One 7 10 2012
35. L.N. Segal, A.V. Alekseyenko, J.C. Clemente, R. Kulkarni, B. Wu, Z. Gao, and et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation Microbiome 1 1 2013
36. K. Borewicz, A.A. Pragman, H.B. Kim, M. Hertz, C. Wendt, and R.E. Isaacson Longitudinal analysis of the lung microbiome in lung transplantation FEMS Microbiol Lett 339 1 2013 57 65
37. R.P. Dickson, J.R. Erb-Downward, H.C. Prescott, F.J. Martinez, J.L. Curtis, V.N. Lama, and et al. Cell-associated bacteria in the human lung microbiome Microbiome 2 2014
38. R.P. Dickson, J.R. Erb-Downward, C.M. Freeman, N. Walker, B.S. Scales, J.M. Beck, and et al. Changes in the lung microbiome following lung transplantation include the emergence of two distinct pseudomonas species with distinct clinical associations PLoS One 9 5 2014
39. R.P. Dickson, J.R. Erb-Downward, H.C. Prescott, F.J. Martinez, J.L. Curtis, V.N. Lama, and et al. Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid J Clin Microbiol 52 10 2014 3605 3613
40. Integrative HMPRNC The integrative human microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease Cell Host Microbe 16 3 2014 276 289
41. H.L. Twigg, A. Morris, E. Ghedin, J.L. Curtis, G.B. Huffnagle, K. Crothers, and et al. Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise Lancet Respir Med 1 5 2013 354 356
42. A. Morris, J.M. Beck, P.D. Schloss, T.B. Campbell, K. Crothers, J.L. Curtis, and et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers Am J Respir Crit Care Med 187 10 2013 1067 1075
43. C. Lozupone, A. Cota-Gomez, B.E. Palmer, D.J. Linderman, E.S. Charlson, E. Sodergren, and et al. Widespread colonization of the lung by tropheryma whipplei in HIV infection Am J Respir Crit Care Med 187 10 2013 1110 1117
44. D. Willner, M. Furlan, M. Haynes, R. Schmieder, F.E. Angly, J. Silva, and et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals PLoS One 4 10 2009
45. F. Lysholm, A. Wetterbom, C. Lindau, H. Darban, A. Bjerkner, K. Fahlander, and et al. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing PLoS One 7 2 2012
46. D. Willner, M.R. Haynes, M. Furlan, N. Hanson, B. Kirby, Y.W. Lim, and et al. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung Am J Respir Cell Mol Biol 46 2 2012 127 131
47. J.C. Young, C. Chehoud, K. Bittinger, A. Bailey, J.M. Diamond, E. Cantu, and et al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients Am J Transplant Off J Am Soc Transpl Am Soc Transpl Surg 15 1 2015 200 209
48. L. Delhaes, S. Monchy, E. Fréalle, C. Hubans, J. Salleron, S. Leroy, and et al. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community - implications for therapeutic management PLoS One 7 4 2012
49. G.B. Huffnagle, and M.C. Noverr The emerging world of the fungal microbiome Trends Microbiol 21 7 2013 334 341
50. S.D. Willger, S.L. Grim, E.L. Dolben, A. Shipunova, T.H. Hampton, H.G. Morrison, and et al. Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis Microbiome 2 1 2014
51. M. Davidson, B. Tempest, and D.L. Palmer Bacteriologic diagnosis of acute pneumonia. Comparison of sputum, transtracheal aspirates, and lung aspirates J Am Med Assoc 235 2 1976 158 163
52. E.B. Matthew, F.M. Holstrom, and R.L. Kaspar A simple method for diagnosing pneumonia in intubated or tracheostomized patients Crit Care Med 5 2 1977 76 81
53. R.P. Dickson, J.R. Erb-Downward, and G.B. Huffnagle The role of the bacterial microbiome in lung disease Expert Rev Respir Med 7 3 2013 245 257
54. S.P. Hubbell Neutral theory in community ecology and the hypothesis of functional equivalence Funct Ecol 19 1 2005 166 172
55. C.M. Bassis, J. E.-D.; R.P. Dickson, C.M. Freeman, T.M. Schmidt, V.B. Young, J.M. Beck, J.L. Curtis, and G.B. Huffnagle Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals MBio 6 2 2015
56. R.P. Dickson, J. E.-D.; C.M. Freeman, L. McCloskey, J.M. Beck, G.B. Huffnagle, and J.L. Curtis Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography Ann Am Thorac Soc 12 6 2015 821 830
57. V.B. Rudkjøbing, T.R. Thomsen, M. Alhede, K.N. Kragh, P.H. Nielsen, U.R. Johansen, and et al. True microbiota involved in chronic lung infection of cystic fibrosis patients found by culturing and 16S rRNA gene analysis J Clin Microbiol 49 12 2011 4352 4355
58. A.F. Goddard, B.J. Staudinger, S.E. Dowd, A. Joshi-Datar, R.D. Wolcott, M.L. Aitken, and et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota Proc Natl Acad Sci USA 109 34 2012 13769 13774
59. R. Cabrera-Rubio, M. Garcia-Núñez, L. Setó, J.M. Antó, A. Moya, E. Monsó, and et al. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease J Clin Microbiol 50 11 2012 3562 3568
60. M. Arumugam, J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D.R. Mende, and et al. Enterotypes of the human gut microbiome Nature 473 7346 2011 174 180
61. D. Knights, T.L. Ward, C.E. McKinlay, H. Miller, A. Gonzalez, D. McDonald, and et al. Rethinking "enterotypes" Cell Host Microbe 16 4 2014 433 437
62. G.L. Hold, M. Smith, C. Grange, E.R. Watt, E.M. El-Omar, and I. Mukhopadhya Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years? World J Gastroenterol WJG 20 5 2014 1192 1210
63. Mandeep S. Jassal, and William R. Bishai Epidemiology and challenges to the elimination of global tuberculosis Clin Infect Dis 50 s3 2010 S156 S164
64. S.M. Querido, G.N. Back-Brito, S.S. Dos Santos, M.V. Leao, C.Y. Koga-Ito, and A.O. Jorge Opportunistic microorganisms in patients undergoing antibiotic therapy for pulmonary tuberculosis Braz J Microbiol 42 4 2011 1321 1328
65. G. Dubourg, J.C. Lagier, F. Armougom, C. Robert, I. Hamad, P. Brouqui, and et al. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics Eur J Clin Microbiol Infect Dis 32 5 2013 637 645
66. K. Winglee, E. Eloe-Fadrosh, S. Gupta, H. Guo, C. Fraser, and W. Bishai Aerosol Mycobacterium tuberculosis infection causes rapid loss of diversity in gut microbiota PLoS One 9 5 2014
67. S. Perry, B.C. de Jong, J.V. Solnick, M. de la Luz Sanchez, S. Yang, P.L. Lin, and et al. Infection with Helicobacter pylori is associated with protection against tuberculosis PLoS One 5 1 2010
68. I.C. Arnold, N. Dehzad, S. Reuter, H. Martin, B. Becher, C. Taube, and et al. Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells J Clin Investig 121 8 2011 3088 3093
69. M. Oertli, M. Sundquist, I. Hitzler, D.B. Engler, I.C. Arnold, S. Reuter, and et al. DC-derived IL-18 drives Treg differentiation, murine helicobacter pylori-specific immune tolerance, and asthma protection J Clin Invest 122 3 2012 1082 1096
70. D.B. Engler, S. Reuter, Y. van Wijck, S. Urban, A. Kyburz, J. Maxeiner, and et al. Effective treatment of allergic airway inflammation with Helicobacter pylori immunomodulators requires BATF3-dependent dendritic cells and IL-10 Proc Natl Acad Sci USA 111 32 2014 11810 11815
71. Z. Cui, Y. Zhou, H. Li, Y. Zhang, S. Zhang, S. Tang, and et al. Complex sputum microbial composition in patients with pulmonary tuberculosis BMC Microbiol 12 2012
72. M.K. Cheung, W.Y. Lam, W.Y. Fung, P.T. Law, C.H. Au, W. Nong, and et al. Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing PLoS One 8 1 2013 e54574
73. L.E. Botero, L. Delgado-Serrano, M.L. Cepeda, J.R. Bustos, J.M. Anzola, P. Del Portillo, and et al. Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis Microbiome 2 2014
74. J. Wu, W. Liu, L. He, F. Huang, J. Chen, P. Cui, and et al. Sputum microbiota associated with new, recurrent and treatment failure tuberculosis PLoS One 8 12 2013
75. N.F. Mistry, Y. Dholakia, D.T. D'Souza, M. Taylor, S. Hoffner, and T.J. Birdi Rhodococcus and Mycobacterium tuberculosis: masquerade or mixed infection Int J Tuberc Lung Dis 10 3 2006 351 353
76. L. Guillot, N. Nathan, O. Tabary, G. Thouvenin, P. Le Rouzic, H. Corvol, and et al. Alveolar epithelial cells: master regulators of lung homeostasis Int J Biochem Cell Biol 45 11 2013 2568 2573
77. O.D. Chuquimia, D.H. Petursdottir, M.J. Rahman, K. Hartl, M. Singh, and C. Fernandez The role of alveolar epithelial cells in initiating and shaping pulmonary immune responses: communication between innate and adaptive immune systems PLoS One 7 2 2012 e32125
78. O.D. Chuquimia, D.H. Petursdottir, N. Periolo, and C. Fernandez Alveolar epithelial cells are critical in protection of the respiratory tract by secretion of factors able to modulate the activity of pulmonary macrophages and directly control bacterial growth Infect Immun 81 1 2013 381 389
79. D.H. Petursdottir, O.D. Chuquimia, R. Freidl, and C. Fernandez Macrophage control of phagocytosed mycobacteria is increased by factors secreted by alveolar epithelial cells through nitric oxide independent mechanisms PLoS One 9 8 2014 e103411
80. M.J. Harriff, M.E. Cansler, K.G. Toren, E.T. Canfield, S. Kwak, M.C. Gold, and et al. Human lung epithelial cells contain Mycobacterium tuberculosis in a late endosomal vacuole and are efficiently recognized by CD8(+) T cells PLoS One 9 5 2014 e97515
81. G. Nouailles, A. Dorhoi, M. Koch, J. Zerrahn, J. Weiner 3rd, K.C. Fae, and et al. CXCL5-secreting pulmonary epithelial cells drive destructive neutrophilic inflammation in tuberculosis J Clin Invest 124 3 2014 1268 1282
82. M. Gengenbacher, and S.H. Kaufmann Mycobacterium tuberculosis: success through dormancy FEMS Microbiol Rev 36 3 2012 514 532
83. E. Pistacchio Flügge's droplets Infez Med 7 2 1999 129 132
84. H. Bruns, and S. Stenger New insights into the interaction of Mycobacterium tuberculosis and human macrophages Future Microbiol 9 3 2014 327 341
85. J.M. Yuk, and E.K. Jo Host immune responses to mycobacterial antigens and their implications for the development of a vaccine to control tuberculosis Clin Exp Vaccine Res 3 2 2014 155 167
86. S.M. Behar, M. Divangahi, and H.G. Remold Evasion of innate immunity by Mycobacterium tuberculosis: is death an exit strategy? Nat Rev Microbiol 8 9 2010 668 674
87. N. van der Wel, D. Hava, D. Houben, D. Fluitsma, M. van Zon, J. Pierson, and et al. M. Tuberculosis and M. leprae translocate from the phagolysosome to the cytosol in myeloid cells Cell 129 7 2007 1287 1298
88. D.A. Keown, D.A. Collings, and J.I. Keenan Uptake and persistence of Mycobacterium avium subsp. Paratuberculosis in human monocytes Infect Immun 80 11 2012 3768 3775
89. T. Soldati, and O. Neyrolles Mycobacteria and the intraphagosomal environment: take it with a pinch of salt(s)! Traffic 13 8 2012 1042 1052
90. A. Rahman, P. Sobia, N. Gupta, L.V. Kaer, and G. Das Mycobacterium tuberculosis subverts the TLR-2-MyD88 pathway to facilitate its translocation into the cytosol PLoS One 9 1 2014 e86886
91. L. Berod, P. Stuve, M. Swallow, C. Arnold-Schrauf, F. Kruse, M.V. Gentilini, and et al. MyD88 signalling in myeloid cells is sufficient to prevent chronic mycobacterial infection Eur J Immunol 44 5 2014 1399 1409
92. C.M. Fremond, V. Yeremeev, D.M. Nicolle, M. Jacobs, V.F. Quesniaux, and B. Ryffel Fatal Mycobacterium tuberculosis infection despite adaptive immune response in the absence of MyD88 J Clin Invest 114 12 2004 1790 1799
93. N. Reiling, S. Ehlers, and C. Holscher MyDths and un-TOLLed truths: sensor, instructive and effector immunity to tuberculosis Immunol Lett 116 1 2008 15 23
94. C. Mu, Y. Yang, and W. Zhu Crosstalk between the immune receptors and gut microbiota Curr Protein Pept Sci 16 1 2015
95. T. Maekawa, J.L. Krauss, T. Abe, R. Jotwani, M. Triantafilou, K. Triantafilou, and et al. Porphyromonas gingivalis manipulates complement and TLR signaling to uncouple bacterial clearance from inflammation and promote dysbiosis Cell Host Microbe 15 6 2014 768 778
96. D.S. Nielsen, L. Krych, K. Buschard, C.H. Hansen, and A.K. Hansen Beyond genetics. Influence of dietary factors and gut microbiota on type 1 diabetes FEBS Lett 588 22 2014 4234 4243
97. D. Bharti, A. Kumar, R.S. Mahla, S. Kumar, H. Ingle, H. Shankar, and et al. The role of TLR9 polymorphism in susceptibility to pulmonary tuberculosis Immunogenetics 66 12 2014 675 681
98. S. Davila, M.L. Hibberd, R. Hari Dass, H.E. Wong, E. Sahiratmadja, C. Bonnard, and et al. Genetic association and expression studies indicate a role of toll-like receptor 8 in pulmonary tuberculosis PLoS Genet 4 10 2008 e1000218
99. J. Basu, D.M. Shin, and E.K. Jo Mycobacterial signaling through toll-like receptors Front Cell Infect Microbiol 2 2012 145
100. D.R. Velez, C. Wejse, M.E. Stryjewski, E. Abbate, W.F. Hulme, J.L. Myers, and et al. Variants in toll-like receptors 2 and 9 influence susceptibility to pulmonary tuberculosis in Caucasians, African-Americans, and West Africans Hum Genet 127 1 2010 65 73
101. S. Thada, V.L. Valluri, and S.L. Gaddam Influence of Toll-like receptor gene polymorphisms to tuberculosis susceptibility in humans Scand J Immunol 78 3 2013 221 229
102. A.L. Kau, P.P. Ahern, N.W. Griffin, A.L. Goodman, and J.I. Gordon Human nutrition, the gut microbiome and the immune system Nature 474 7351 2011 327 336
103. H. Chung, S.J. Pamp, J.A. Hill, N.K. Surana, S.M. Edelman, E.B. Troy, and et al. Gut immune maturation depends on colonization with a host-specific microbiota Cell 149 7 2012 1578 1593
104. J. Duan, H. Chung, E. Troy, and D.L. Kasper Microbial colonization drives expansion of IL-1 receptor 1-expressing and IL-17-producing gamma/delta T cells Cell Host Microbe 7 2 2010 140 150
105. G. Wingender, D. Stepniak, P. Krebs, L. Lin, S. McBride, B. Wei, and et al. Intestinal microbes affect phenotypes and functions of invariant natural killer T cells in mice Gastroenterology 143 2 2012 418 428
106. S.K. Lathrop, S.M. Bloom, S.M. Rao, K. Nutsch, C.W. Lio, N. Santacruz, and et al. Peripheral education of the immune system by colonic commensal microbiota Nature 478 7368 2011 250 254
107. A.J. Macpherson, and T. Uhr Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria Science 303 5664 2004 1662 1665
108. G. Zhang, R. Chen, and J.D. Rudney Streptococcus cristatus attenuates fusobacterium nucleatum-induced interleukin-8 expression in oral epithelial cells J Periodontal Res 43 4 2008 408 416
109. T. Olszak, D. An, S. Zeissig, M.P. Vera, J. Richter, A. Franke, and et al. Microbial exposure during early life has persistent effects on natural killer T cell function Science 336 6080 2012 489 493
110. G.E. Diehl, R.S. Longman, J.X. Zhang, B. Breart, C. Galan, A. Cuesta, and et al. Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX(3)CR1(hi) cells Nature 494 7435 2013 116 120
111. E.S. Gollwitzer, and B.J. Marsland Microbiota abnormalities in inflammatory airway diseases - potential for therapy Pharmacol Ther 141 1 2014 32 39
112. T.B. Clarke Early innate immunity to bacterial infection in the lung is regulated systemically by the commensal microbiota via nod-like receptor ligands Infect Immun 82 11 2014 4596 4606
113. A. Legatzki, B. Rösler, and E. von Mutius Microbiome diversity and asthma and allergy risk Curr Allergy Asthma Rep 14 10 2014
114. H. Bisgaard, N. Li, K. Bonnelykke, B.L.K. Chawes, T. Skov, G. Paludan-Müller, and et al. Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age J Allergy Clin Immunol 128 3 2011 646 652 e641-645
115. M.J. Ege, M. Mayer, A.C. Normand, J. Genuneit, W.O. Cookson, C. Braun-Fahrlander, and et al. Exposure to environmental microorganisms and childhood asthma N Engl J Med 364 8 2011 701 709
116. C. Petersen, and J.L. Round Defining dysbiosis and its influence on host immunity and disease Cell Microbiol 16 7 2014 1024 1033
117. J. Qin, Y. Li, Z. Cai, S. Li, J. Zhu, F. Zhang, and et al. A metagenome-wide association study of gut microbiota in type 2 diabetes Nature 490 7418 2012 55 60
118. M.E. Mejia-Leon, J.F. Petrosino, N.J. Ajami, M.G. Dominguez-Bello, and A.M. de la Barca Fecal microbiota imbalance in mexican children with type 1 diabetes Sci Rep 4 2014 3814
119. H. Tilg, and A.R. Moschen Microbiota and diabetes: an evolving relationship Gut 63 9 2014 1513 1521
120. B.I. Restrepo, and L.S. Schlesinger Impact of diabetes on the natural history of tuberculosis Diabetes Res Clin Pract 106 2 2014 191 199
121. L.B. Rawal, R.J. Tapp, E.D. Williams, C. Chan, S. Yasin, and B. Oldenburg Prevention of type 2 diabetes and its complications in developing countries: a review Int J Behav Med 19 2 2012 121 133
122. M.O. Moraes, A.G. Pacheco, J.J. Schonkeren, P.R. Vanderborght, J.A. Nery, A.R. Santos, and et al. Interleukin-10 promoter single-nucleotide polymorphisms as markers for disease susceptibility and disease severity in leprosy Genes Immun 5 7 2004 592 595
123. B. Liang, Y. Guo, Y. Li, and H. Kong Association between IL-10 gene polymorphisms and susceptibility of tuberculosis: evidence based on a meta-analysis PLoS One 9 2 2014 e88448
124. C.M. Stein, S. Zalwango, A.B. Chiunda, C. Millard, D.V. Leontiev, A.L. Horvath, and et al. Linkage and association analysis of candidate genes for TB and TNFalpha cytokine expression: evidence for association with IFNGR1, IL-10, and TNF receptor 1 genes Hum Genet 121 6 2007 663 673
125. R.J. Wilkinson, M. Llewelyn, Z. Toossi, P. Patel, G. Pasvol, A. Lalvani, and et al. Influence of vitamin D deficiency and vitamin D receptor polymorphisms on tuberculosis among Gujarati Asians in west London: a case-control study Lancet 355 9204 2000 618 621
126. J. Weinzirl The action of sunlight upon bacteria with special reference to B. Tuberculosis Public Health Pap Rep 32 Pt 2 1906 128 153
127. P.T. Liu, S. Stenger, H. Li, L. Wenzel, B.H. Tan, S.R. Krutzik, and et al. Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response Science 311 5768 2006 1770 1773
128. K. Afsal, M. Harishankar, V.V. Banurekha, N. Meenakshi, R.T. Parthasarathy, and P. Selvaraj Effect of 1,25-dihydroxy vitamin D on cathelicidin expression in patients with and without cavitary tuberculosis Tuberc (Edinb) 94 6 2014 599 605
129. A.M. van der Does, P. Bergman, B. Agerberth, and L. Lindbom Induction of the human cathelicidin LL-37 as a novel treatment against bacterial infections J Leukoc Biol 92 4 2012 735 742
130. V. Lievin-Le Moal, and A.L. Servin The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota Clin Microbiol Rev 19 2 2006 315 337
131. J.S. Khara, Y. Wang, X.Y. Ke, S. Liu, S.M. Newton, P.R. Langford, and et al. Anti-mycobacterial activities of synthetic cationic alpha-helical peptides and their synergism with rifampicin Biomaterials 35 6 2014 2032 2038
132. Y. Lan, J.T. Lam, G.K. Siu, W.C. Yam, A.J. Mason, and J.K. Lam Cationic amphipathic D-enantiomeric antimicrobial peptides with in vitro and ex vivo activity against drug-resistant Mycobacterium tuberculosis Tuberc (Edinb) 94 6 2014 678 689
133. A. Padhi, M. Sengupta, S. Sengupta, K.H. Roehm, and A. Sonawane Antimicrobial peptides and proteins in mycobacterial therapy: current status and future prospects Tuberc (Edinb) 94 4 2014 363 373
134. J.H. Ooi, Y. Li, C.J. Rogers, and M.T. Cantorna Vitamin D regulates the gut microbiome and protects mice from dextran sodium sulfate-induced colitis J Nutr 143 10 2013 1679 1686
135. J. Chen, A. Waddell, Y.D. Lin, and M.T. Cantorna Dysbiosis caused by vitamin D receptor deficiency confers colonization resistance to Citrobacter rodentium through modulation of innate lymphoid cells Mucosal Immunol 8 3 2014 618 626
136. V. Mai, Q.M. McCrary, R. Sinha, and M. Glei Associations between dietary habits and body mass index with gut microbiota composition and fecal water genotoxicity: an observational study in African American and caucasian American volunteers Nutr J 8 2009 49
137. R. Feng, Y. Li, G. Li, Z. Li, Y. Zhang, Q. Li, and et al. Lower serum 25 (OH) D concentrations in type 1 diabetes: a meta-analysis Diabetes Res Clin Pract 108 3 2015 e71 75
138. C. Mathieu Vitamin D and diabetes: where do we stand? Diabetes Res Clin Pract 108 2 2015 201 209
139. Y.X. Li, and L. Zhou Vitamin D deficiency, obesity and diabetes Cell Mol Biol (Noisy-le-grand) 61 3 2015 35 38
140. A.E. Handel, and S.V. Ramagopalan Tuberculosis and diabetes mellitus: is vitamin D the missing link? Lancet Infect Dis 10 9 2010 596
141. N. Lopez-Lopez, I. Gonzalez-Curiel, J. Castaneda-Delgado, A. Montoya-Rosales, B. Gandara-Jasso, J.A. Enciso-Moreno, and et al. Vitamin D supplementation promotes macrophages' anti-mycobacterial activity in type 2 diabetes mellitus patients with low vitamin D receptor expression Microbes Infect 16 9 2014 755 761
142. Q. Wang, A. Ma, I.C. Bygbjerg, X. Han, Y. Liu, S. Zhao, and et al. Rationale and design of a randomized controlled trial of the effect of retinol and vitamin D supplementation on treatment in active pulmonary tuberculosis patients with diabetes BMC Infect Dis 13 2013 104
143. B.L. Cantarel, E. Waubant, C. Chehoud, J. Kuczynski, T.Z. DeSantis, J. Warrington, and et al. Gut microbiota in multiple sclerosis: possible influence of immunomodulators J Investig Med 63 5 2015 729 734
144. A. Assa, L. Vong, L.J. Pinnell, N. Avitzur, K.C. Johnson-Henry, and P.M. Sherman Vitamin D deficiency promotes epithelial barrier dysfunction and intestinal inflammation J Infect Dis 210 8 2014 1296 1305