1. Turner PV. The role of the gut microbiota on animal model reproducibility. Animal Model Exp Med 2018;1:109–115.

2. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999;69:1035S–1045S.

3. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006;124:837–848.

4. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science 2012;336:1268–1273.

5. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J 2017;474:1823–1836.

6. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med 2016;375:2369–2379.

7. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ 2018;361:k2179.

8. Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science 2016;Apr. 29. 352(6285):539–44.

9. Celebi Sozener Z, Ozdel Ozturk B, Cerci P, et al. Epithelial barrier hypothesis: effect of the external exposome on the microbiome and epithelial barriers in allergic disease. Allergy 2022;77:1418–1449.

10. Sohn KH, Baek MG, Choi SM, et al. Alteration of lung and gut microbiota in IL-13-transgenic mice simulating chronic asthma. J Microbiol Biotechnol 2020;30:1819–1826.

11. Brusselle GG, Koppelman GH. Biologic therapies for severe asthma. N Engl J Med 2022;386:157–171.

12. Herbst T, Sichelstiel A, Schär C, et al. Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am J Respir Crit Care Med 2011;184:198–205.

13. Remot A, Descamps D, Noordine ML, et al. Bacteria isolated from lung modulate asthma susceptibility in mice. ISME J 2017;11:1061–1074.

14. van Nimwegen FA, Penders J, Stobberingh EE, et al. Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. J Allergy Clin Immunol 2011;128:948–955e1-e3.

15. Johnson CC, Ownby DR, Alford SH, et al. Antibiotic exposure in early infancy and risk for childhood atopy. J Allergy Clin Immunol 2005;115:1218–1224.

16. Fujimura KE, Sitarik AR, Havstad S, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med 2016;22:1187–1191.

17. Arrieta MC, Stiemsma LT, Dimitriu PA, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 2015;7:307ra152.

18. Begley L, Madapoosi S, Opron K, et al. Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study. BMJ Open Respir Res 2018;5:e000324.

19. Fujimura KE, Demoor T, Rauch M, et al. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A 2014;111:805–810.

20. Johansson MA, Sjögren YM, Persson JO, Nilsson C, Sverremark-Ekström E. Early colonization with a group of Lactobacilli decreases the risk for allergy at five years of age despite allergic heredity. PLoS One 2011;6:e23031.

21. Sagar S, Morgan ME, Chen S, et al. Bifidobacterium breve and Lactobacillus rhamnosus treatment is as effective as budesonide at reducing inflammation in a murine model for chronic asthma. Respir Res 2014;15:46.

22. Raftis EJ, Delday MI, Cowie P, et al. Bifidobacterium breve MRx0004 protects against airway inflammation in a severe asthma model by suppressing both neutrophil and eosinophil lung infiltration. Sci Rep 2018;8:12024.

23. Sagar S, Vos AP, Morgan ME, et al. The combination of Bifidobacterium breve with non-digestible oligosaccharides suppresses airway inflammation in a murine model for chronic asthma. Biochim Biophys Acta 2014;1842:573–583.

24. 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):232–6.

25. O’Mahony C, Scully P, O’Mahony D, et al. Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-kappaB activation. PLoS Pathog 2008;4:e1000112.

26. de Groot P, Nikolic T, Pellegrini S, et al. Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Gut 2021;70:92–105.

27. Karimi K, Inman MD, Bienenstock J, Forsythe P. Lactobacillus reuteri-induced regulatory T cells protect against an allergic airway response in mice. Am J Respir Crit Care Med 2009;179:186–193.

28. Li YN, Huang F, Liu L, Qiao HM, Li Y, Cheng HJ. Effect of oral feeding with Clostridium leptum on regulatory T-cell responses and allergic airway inflammation in mice. Ann Allergy Asthma Immunol 2012;109:201–207.

29. Michalovich D, Rodriguez-Perez N, Smolinska S, et al. Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients. Nat Commun 2019;10:5711.

30. Demirci M, Tokman HB, Uysal HK, et al. Reduced Akkermansia muciniphila and Faecalibacterium prausnitzii levels in the gut microbiota of children with allergic asthma. Allergol Immunopathol (Madr) 2019;47:365–371.

31. Penders J, Thijs C, Vink C, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006;118:511–521.

32. Roduit C, Frei R, Ferstl R, et al. High levels of butyrate and propionate in early life are associated with protection against atopy. Allergy 2019;74:799–809.

33. Di Vincenzo F, Puca P, Lopetuso LR, et al. Bile acid-related regulation of mucosal inflammation and intestinal motility: from pathogenesis to therapeutic application in IBD and microscopic colitis. Nutrients 2022;14:2664.

34. Joyce SA, Gahan CG. Disease-associated changes in bile acid profiles and links to altered gut microbiota. Dig Dis 2017;35:169–177.

35. Willart MA, van Nimwegen M, Grefhorst A, et al. Ursodeoxycholic acid suppresses eosinophilic airway inflammation by inhibiting the function of dendritic cells through the nuclear farnesoid X receptor. Allergy 2012;67:1501–1510.

36. Nakada EM, Bhakta NR, Korwin-Mihavics BR, et al. Conjugated bile acids attenuate allergen-induced airway inflammation and hyperresponsiveness by inhibiting UPR transducers. JCI Insight 2019;4:e98101.

37. Kelly RS, Sordillo JE, Lasky-Su J, et al. Plasma metabolite profiles in children with current asthma. Clin Exp Allergy 2018;48:1297–1304.

38. Comhair SA, McDunn J, Bennett C, Fettig J, Erzurum SC, Kalhan SC. Metabolomic endotype of asthma. J Immunol 2015;195:643–650.

39. Mantis NJ, Rol N, Corthésy B. Secretory IgA’s complex roles in immunity and mucosal homeostasis in the gut. Mucosal Immunol 2011;4:603–611.

40. Hapfelmeier S, Lawson MA, Slack E, et al. Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science 2010;328:1705–1709.

41. Nakajima A, Vogelzang A, Maruya M, et al. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med 2018;215:2019–2034.

42. Kilian M, Reinholdt J, Lomholt H, Poulsen K, Frandsen EV. Biological significance of IgA1 proteases in bacterial colonization and pathogenesis: critical evaluation of experimental evidence. APMIS 1996;104:321–338.

43. Wang X, Zhang J, Wu Y, Xu Y, Zheng J. SIgA in various pulmonary diseases. Eur J Med Res 2023;28:299.

44. Gu BH, Choi JP, Park T, et al. Adult asthma with symptomatic eosinophilic inflammation is accompanied by alteration in gut microbiome. Allergy 2023;78:1909–1921.

45. Sohn KH, Choi S, Jung JW, et al. Different inflammatory features of asthma according to gut microbiome enterotype. Allergy 2023;78:2997–3001.

46. Rabe KF, Watz H. Chronic obstructive pulmonary disease. Lancet 2017;389:1931–1940.

47. Quan Y, Yin Z, Chen S, et al. The gut-lung axis: gut microbiota changes associated with pulmonary fibrosis in mouse models induced by bleomycin. Front Pharmacol 2022;13:985223.

48. Bowerman KL, Rehman SF, Vaughan A, et al. Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nat Commun 2020;11:5886.

49. Lee SH, Yun Y, Kim SJ, et al. Association between cigarette smoking status and composition of gut microbiota: population-based cross-sectional study. J Clin Med 2018;7:282.

50. Tanner L, Single AB. Animal models reflecting chronic obstructive pulmonary disease and related respiratory disorders: translating pre-clinical data into clinical relevance. J Innate Immun 2020;12:203–225.

51. Li N, Dai Z, Wang Z, et al. Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. Respir Res 2021;22:274.

52. Lai HC, Lin TL, Chen TW, et al. Gut microbiota modulates COPD pathogenesis: role of anti-inflammatory Parabacteroides goldsteinii lipopolysaccharide. Gut 2022;71:309–321.

53. Liu Y, Teo SM, Méric G, et al. The gut microbiome is a significant risk factor for future chronic lung disease. J Allergy Clin Immunol 2023;151:943–952.

54. Molyneaux PL, Cox MJ, Willis-Owen SA, et al. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2014;190:906–913.

55. Molyneaux PL, Cox MJ, Wells AU, et al. Changes in the respiratory microbiome during acute exacerbations of idiopathic pulmonary fibrosis. Respir Res 2017;18:29.

56. Han MK, Zhou Y, Murray S, et al. Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med 2014;2:548–556.

57. Chioma OS, Mallott EK, Chapman A, et al. Gut microbiota modulates lung fibrosis severity following acute lung injury in mice. Commun Biol 2022;5:1401.

58. Durack J, Kimes NE, Lin DL, et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat Commun 2018;9:707.

59. Dzidic M, Abrahamsson TR, Artacho A, et al. Aberrant IgA responses to the gut microbiota during infancy precede asthma and allergy development. J Allergy Clin Immunol 2017;139:1017–1025.e14.

60. Liu Y, Tran DQ, Rhoads JM. Probiotics in disease prevention and treatment. J Clin Pharmacol 2018;58 Suppl 10(Suppl 10):S164–S179.

61. Wang W, Luo X, Zhang Q, He X, Zhang Z, Wang X. Bifidobacterium infantis relieves allergic asthma in mice by regulating Th1/Th2. Med Sci Monit 2020;26:e920583.

62. Navarro S, Cossalter G, Chiavaroli C, et al. The oral administration of bacterial extracts prevents asthma via the recruitment of regulatory T cells to the airways. Mucosal Immunol 2011;4:53–65.

63. Wu Z, Mehrabi Nasab E, Arora P, Athari SS. Study effect of probiotics and prebiotics on treatment of OVA-LPS-induced of allergic asthma inflammation and pneumonia by regulating the TLR4/NF-kB signaling pathway. J Transl Med 2022;20:130.

64. Antunes KH, Fachi JL, de Paula R, et al. Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response. Nat Commun 2019;10:3273.

65. Trompette A, Gollwitzer ES, Yadava K, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014;20:159–166.

66. Vieira RS, Castoldi A, Basso PJ, Hiyane MI, Câmara NOS, Almeida RR. Butyrate attenuates lung inflammation by negatively modulating Th9 cells. Front Immunol 2019;10:67.

67. Park HK, Choi Y, Lee DH, et al. Altered gut microbiota by azithromycin attenuates airway inflammation in allergic asthma. J Allergy Clin Immunol 2020;145:1466–1469.e8.

68. Wei S, Mortensen MS, Stokholm J, et al. Short- and longterm impacts of azithromycin treatment on the gut microbiota in children: a double-blind, randomized, placebo-controlled trial. EBioMedicine 2018;38:265–272.

69. Trivedi R, Barve K. Gut microbiome a promising target for management of respiratory diseases. Biochem J 2020;477:2679–2696.

70. Shah P, Fritz JV, Glaab E, et al. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun 2016;7:11535.

71. Gibson GR, Hutkins R, Sanders ME, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 2017;14:491–502.

72. Williams NT. Probiotics. Am J Health Syst Pharm 2010;67:449–458.

73. Ramakrishna BS. Role of the gut microbiota in human nutrition and metabolism. J Gastroenterol Hepatol 2013;28 Suppl 4:9–17.

74. Matsusaki T, Takeda S, Takeshita M, et al. Augmentation of T helper type 1 immune response through intestinal immunity in murine cutaneous herpes simplex virus type 1 infection by probiotic Lactobacillus plantarum strain 06CC2. Int Immunopharmacol 2016;39:320–327.

75. Won TJ, Kim B, Song DS, et al. Modulation of Th1/Th2 balance by Lactobacillus strains isolated from Kimchi via stimulation of macrophage cell line J774A.1 in vitro. J Food Sci 2011;76:H55–H61.

76. Lee DH, Park HK, Lee HR, et al. Immunoregulatory effects of Lactococcus lactis-derived extracellular vesicles in allergic asthma. Clin Transl Allergy 2022;12:e12138.

77. Bermudez-Brito M, Plaza-Díaz J, Muñoz-Quezada S, Gómez-Llorente C, Gil A. Probiotic mechanisms of action. Ann Nutr Metab 2012;61:160–174.

78. Fernando WMADB, Flint SH, Ranaweera KKDS, Bamunuarachchi A, Johnson SK, Brennan CS. The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation. Int J Food Sci Nutr 2018;69:144–154.

79. Niessen NM, Gibson PG, Simpson JL, Scott HA, Baines KJ, Fricker M. Airway monocyte modulation relates to tumour necrosis factor dysregulation in neutrophilic asthma. ERJ Open Res 2021;7:00131–2021.

80. Niessen NM, Gibson PG, Baines KJ, et al. Sputum TNF markers are increased in neutrophilic and severe asthma and are reduced by azithromycin treatment. Allergy 2021;76:2090–2101.

81. Korpela K, Salonen A, Virta LJ, et al. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat Commun 2016;7:10410.

82. Kelly CJ, Zheng L, Campbell EL, et al. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 2015;17:662–671.

83. Furusawa Y, Obata Y, Fukuda S, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013;504:446–450.

84. Zelante T, Iannitti RG, Cunha C, et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 2013;39:372–385.

85. Viladomiu M, Hontecillas R, Bassaganya-Riera J. Modulation of inflammation and immunity by dietary conjugated linoleic acid. Eur J Pharmacol 2016;785:87–95.

86. Sun M, Wu W, Liu Z, Cong Y. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. J Gastroenterol 2017;52:1–8.

87. Wong AC, Levy M. New approaches to microbiome-based therapies. mSystems 2019;4:e00122.

88. Cait A, Hughes MR, Antignano F, et al. Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids. Mucosal Immunol 2018;11:785–795.

89. Lee-Sarwar KA, Kelly RS, Lasky-Su J, et al. Fecal short-chain fatty acids in pregnancy and offspring asthma and allergic outcomes. Fecal short-chain fatty acids in pregnancy and offspring asthma and allergic outcomes 2020;8:1100–1102.e13.

90. Levy M, Thaiss CA, Zeevi D, et al. Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. cell 2015;163:1428–1443.