Man WH, de Steenhuijsen Piters WAA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259–70.

Article  CAS  Google Scholar 

Campbell CD, Barnett C, Sulaiman I. A clinicians’ review of the respiratory microbiome. Breathe [Internet]. 2022 [cited 2022 Jun 28];18(1). Available from: https://breathe.ersjournals.com/content/18/1/210161.

Paudel KR, Dharwal V, Patel VK, Galvao I, Wadhwa R, Malyla V, et al. Role of lung microbiome in innate immune response associated with chronic lung diseases. Front Med. 2020;18(7):554.

Article  Google Scholar 

Rinschen MM, Ivanisevic J, Giera M, Siuzdak G. Identification of bioactive metabolites using activity metabolomics. Nat Rev Mol Cell Biol. 2019;20(6):353–67.

Article  CAS  Google Scholar 

•• Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol. 2022;20(3):143–60. Excellent explanation about the basics of mass spectrometry, from metabolite detection to metabolite annotation and data analysis in microbiome studies.

Article  CAS  Google Scholar 

Hammad H, Lambrecht BN. The basic immunology of asthma. Cell. 2021;184(6):1469–85.

Article  CAS  Google Scholar 

Kuruvilla ME, Lee FEH, Lee GB. Understanding asthma phenotypes, endotypes, and mechanisms of disease. Clin Rev Allergy Immunol. 2019;56(2):219–33.

Article  Google Scholar 

Ver Heul A, Planer J, Kau AL. The human microbiota and asthma. Clin Rev Allergy Immunol. 2019;57(3):350–63.

Article  Google Scholar 

Losol P, Choi JP, Kim SH, Chang YS. The role of upper airway microbiome in the development of adult asthma. Immune Netw [Internet]. 2021 [cited 2022 Jun 29];21(3). https://doi.org/10.4110/in.2021.21.e19.

Wang C, Jiang S, Zhang S, Ouyang Z, Wang G, Wang F. Research progress of metabolomics in asthma. Metabolites. 2021;11(9):567.

Article  Google Scholar 

Santos A, Pité H, Chaves-Loureiro C, Rocha SM, Taborda-Barata L. Metabolic phenotypes in asthmatic adults: relationship with inflammatory and clinical phenotypes and prognostic implications. Metabolites. 2021;11(8):534.

Article  CAS  Google Scholar 

Chen M, He S, Miles P, Li C, Ge Y, Yu X, et al. Nasal bacterial microbiome differs between healthy controls and those with asthma and allergic rhinitis. Front Cell Infect Microbiol. 2022;12:841995.

Article  Google Scholar 

McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, et al. Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma. J Allergy Clin Immunol. 2019;144(5):1187–97.

Article  Google Scholar 

Zhou Y, Jackson D, Bacharier LB, Mauger D, Boushey H, Castro M, et al. The upper-airway microbiota and loss of asthma control among asthmatic children. Nat Commun. 2019;10(1):5714.

Article  CAS  Google Scholar 

Liang Y, Gai XY, Chang C, Zhang X, Wang J, Li TT. Metabolomic profiling differences among asthma, COPD, and healthy subjects: a LC-MS-based metabolomic analysis. Biomed Environ Sci BES. 2019;32(9):659–72.

CAS  Google Scholar 

Liu Y, Zhang X, Zhang L, Oliver BG, Wang HG, Liu ZP, et al. Sputum metabolomic profiling reveals metabolic pathways and signatures associated with inflammatory phenotypes in patients with asthma. Allergy Asthma Immunol Res. 2022;14(4):393–411.

Article  CAS  Google Scholar 

Carraro S, Di Palmo E, Licari A, Barni S, Caldarelli V, De Castro G, et al. Metabolomics to identify omalizumab responders among children with severe asthma: a prospective study. Allergy [Internet]. [cited 2022 Aug 30];n/a(n/a). Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/all.15385.

•• Cait A, Hughes MR, Antignano F, Cait J, Dimitriu PA, Maas KR, et al. Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids. Mucosal Immunol. 2018;11(3):785–95. A study showing that treatment with bacteria-derived SCFAs reduces asthma severity in vivo.

Article  CAS  Google Scholar 

Dong Y, Yan H, Zhao X, Lin R, Lin L, Ding Y, et al. Gu-Ben-Fang-Xiao Decoction ameliorated murine asthma in remission stage by modulating microbiota-acetate-Tregs axis. Front Pharmacol [Internet]. 2020 [cited 2022 Sep 2];11. Available from: https://www.frontiersin.org/articles/10.3389/fphar.2020.00549.

Hufnagl K, Pali-Schöll I, Roth-Walter F, Jensen-Jarolim E. Dysbiosis of the gut and lung microbiome has a role in asthma. Semin Immunopathol. 2020;42(1):75–93.

Article  Google Scholar 

Enaud R, Prevel R, Ciarlo E, Beaufils F, Wieërs G, Guery B, et al. The gut-lung axis in health and respiratory diseases: a place for inter-organ and inter-kingdom crosstalks. Front Cell Infect Microbiol [Internet]. 2020 [cited 2022 Aug 30];10. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2020.00009.

Barcik W, Boutin RCT, Sokolowska M, Finlay BB. The role of lung and gut microbiota in the pathology of asthma. Immunity. 2020;52(2):241–55.

Article  CAS  Google Scholar 

Chiu C, Cheng M, Chiang M, Kuo Y, Tsai M, Chiu C, et al. Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma. Pediatr Allergy Immunol. 2019;30(7):689–97.

Article  Google Scholar 

Comhair SAA, McDunn J, Bennett C, Fetig J, Erzurum SC, Kalhan SC. Metabolomic endotype of asthma. J Immunol Baltim Md 1950. 2015;195(2):643–50.

CAS  Google Scholar 

Gabet S, Rancière F, Just J, de Blic J, Lezmi G, Amat F, et al. Asthma and allergic rhinitis risk depends on house dust mite specific IgE levels in PARIS birth cohort children. World Allergy Organ J. 2019;12(9):100057.

Article  Google Scholar 

Zheng P, Zhang K, Lv X, Liu C, Wang Q, Bai X. Gut microbiome and metabolomics profiles of allergic and non-allergic childhood asthma. J Asthma Allergy. 2022;15:419–35.

Article  CAS  Google Scholar 

Branco ACCC, Yoshikawa FSY, Pietrobon AJ, Sato MN. Role of histamine in modulating the immune response and inflammation. Mediators Inflamm. 2018;27(2018):9524075.

Google Scholar 

Roopashree PG, Shetty SS, Suchetha KN. Effect of medium chain fatty acid in human health and disease. J Funct Foods. 2021;1(87):104724.

Article  Google Scholar 

Lee-Sarwar KA, Kelly RS, Lasky-Su J, Zeiger RS, O’Connor GT, Sandel MT, et al. Integrative analysis of the intestinal metabolome of childhood asthma. J Allergy Clin Immunol. 2019;144(2):442–54.

Article  CAS  Google Scholar 

Anand S, Mande SS. Diet, microbiota and gut-lung connection. Front Microbiol [Internet]. 2018 [cited 2022 Sep 9];9. Available from: https://www.frontiersin.org/articles/https://doi.org/10.3389/fmicb.2018.02147.

Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P, et al. Emerging pathogenic links between microbiota and the gut–lung axis. Nat Rev Microbiol. 2017;15(1):55–63.

Article  CAS  Google Scholar 

Shi J, Yang Y, Xie H, Wang X, Wu J, Long J, et al. Association of oral microbiota with lung cancer risk in a low-income population in the Southeastern USA. Cancer Causes Control CCC. 2021;32(12):1423–32.

Article  Google Scholar 

Pu CY, Seshadri M, Manuballa S, Yendamuri S. The oral microbiome and lung diseases. Curr Oral Health Rep. 2020;7(1):79–86.

Article  Google Scholar 

Chiu CY, Cheng ML, Chiang MH, Wang CJ, Tsai MH, Lin G. Integrated metabolic and microbial analysis reveals host–microbial interactions in IgE-mediated childhood asthma. Sci Rep. 2021;11(1):23407.

Article  CAS  Google Scholar 

•• Chiu CY, Chou HC, Chang LC, Fan WL, Dinh MCV, Kuo YL, et al. Integration of metagenomics-metabolomics reveals specific signatures and functions of airway microbiota in mite-sensitized childhood asthma. Allergy. 2020;75(11):2846–57. The only study in the review that integrated respiratory shotgun metagenomic data with systemic metabolomics.

Article  CAS  Google Scholar 

Nambiar S, Bong How S, Gummer J, Trengove R, Moodley Y. Metabolomics in chronic lung diseases. Respirology. 2020;25(2):139–48.

Article  Google Scholar 

Dean DA, Klechka L, Hossain E, Parab AR, Eaton K, Hinsdale M, et al. Spatial metabolomics reveals localized impact of influenza virus infection on the lung tissue metabolome. mSystems. 2022;0(0):e00353-22.

Google Scholar 

Debik J, Euceda LR, Lundgren S, von der Gythfeldt HL, Garred Ø, Borgen E, et al. Assessing treatment response and prognosis by serum and tissue metabolomics in breast cancer patients. J Proteome Res. 2019;18(10):3649–60.

Article  CAS  Google Scholar 

Schoeman JC, Harms AC, van Weeghel M, Berger R, Vreeken RJ, Hankemeier T. Development and application of a UHPLC–MS/MS metabolomics based comprehensive systemic and tissue-specific screening method for inflammatory, oxidative and nitrosative stress. Anal Bioanal Chem. 2018;410(10):2551–68.

Article  CAS  Google Scholar 

Callejón-Leblic B, García-Barrera T, Pereira-Vega A, Gómez-Ariza JL. Metabolomic study of serum, urine and bronchoalveolar lavage fluid based on gas chromatography mass spectrometry to delve into the pathology of lung cancer. J Pharm Biomed Anal. 2019;30(163):122–9.

Article  Google Scholar 

Wang T, Lin S, Liu R, Li H, Liu Z, Zhang X, et al. Metabolomic profile perturbations of serum, lung, bronchoalveolar lavage fluid, spleen and feces in LPS-induced acute lung injury rats based on HPLC-ESI-QTOF-MS. Anal Bioanal Chem. 2020;412(5):1215–34.

Article  CAS  Google Scholar 

Ghosh N, Choudhury P, Joshi M, Bhattacharyya P, Roychowdhury S, Banerjee R, et al. Global metabolome profiling of exhaled breath condensates in male smokers with asthma COPD overlap and prediction of the disease. Sci Rep. 2021;11(1):16664.

Article  CAS  Google Scholar 

Liang L, Hu M, Chen Y, Liu L, Wu L, Hang C, et al. Metabolomics of bronchoalveolar lavage in children with persistent wheezing. Respir Res. 2022;23(1):161.

Article  CAS  Google Scholar 

Henig NR, Tonelli MR, Pier MV, Burns JL, Aitken ML. Sputum induction as a research tool for sampling the airways of subjects with cystic fibrosis. Thorax. 2001;56(4):306–11.

Article  CAS  Google Scholar 

Patsiris S, Exarchos T, Vlamos P. Exhaled breath condensate (EBC): is it a viable source of biomarkers for lung diseases? Adv Exp Med Biol. 2020;1195:13–8.

Article  CAS  Google Scholar 

Hunt J. Exhaled breath condensate—an overview. Immunol Allergy Clin North Am. 2007;27(4):587–v.

Article  Google Scholar 

Zamuruyev KO, Borras E, Pettit DR, Aksenov AA, Simmons JD, Weimer BC, et al. Effect of temperature control on the metabolite content in exhaled breath condensate. Anal Chim Acta. 2018;2(1006):49–60.

Article  Google Scholar 

Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, et al. Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. Eur Respir J [Internet]. 2021 Jul 1 [cited 2022 Aug 8];58(1). Available from: https://erj.ersjournals.com/content/58/1/2003434.

Ahmed B, Cox MJ, Cuthbertson L, James PL, Cookson WOC, Davies JC, et al. Comparison of the upper and lower airway microbiota in children with chronic lung diseases. PLoS ONE. 2018;13(8):e0201156.

Article  Google Scholar 

Kumpitsch C, Koskinen K, Schöpf V, Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease. BMC Biol. 2019;17(1):87.

Article  Google Scholar 

Tiotiu AI, Novakova P, Nedeva D, Chong-Neto HJ, Novakova S, Steiropoulos P, et al. Impact of air pollution on asthma outcomes. Int J Environ Res Public Health. 2020;17(17):6212.