A scoping review of longitudinal airway microbiota studies

References

• Mayhew D, Devos N, Lambert C, et al. Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations. Thorax. 2018;73(5):422–430.
   PubMed Web of Science ®Google Scholar
• Wang Z, Bafadhel M, Haldar K, et al. Lung microbiome dynamics in COPD exacerbations. Eur Respirat J. 2016;47(4):1082–1092.
   PubMed Web of Science ®Google Scholar
• Hoggard M, Biswas K, Zoing M, et al., editors. Evidence of microbiota dysbiosis in chronic rhinosinusitis. Wiley Online Library: Int Forum Allergy Rhinol; 2017.
   Google Scholar
• Bachert C, Marple B, Schlosser RJ, et al. Adult chronic rhinosinusitis. Nat Rev Dis Primers. 2020;6(1):1–19.
   PubMed Web of Science ®Google Scholar
• Cox MJ, Turek EM, Hennessy C, et al. Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients. PloS One. 2017;12(2):2.
   Web of Science ®Google Scholar
• Goggin RK, Bennett CA, Bassiouni A, et al. Comparative viral sampling in the sinonasal passages; different viruses at different sites. Front Cell Infect Microbiol. 2018;8:334.
   PubMed Web of Science ®Google Scholar
• Bodein A, Chapleur O, Droit A, et al. A generic multivariate framework for the integration of microbiome longitudinal studies with other data types. Front Genet. 2019. p. 10
   PubMed Web of Science ®Google Scholar
• Wagner Mackenzie B, Chang K, Zoing M, et al. Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity. Sci Rep. 2019;9(1):1–10.
   PubMed Web of Science ®Google Scholar
• Tricco AC, Lillie E, Zarin W, et al. PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann Intern Med. 2018;169(7):467–473.
   PubMed Web of Science ®Google Scholar
• Chu DM, Ma J, Prince AL, et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nature Med. 2017;23(3):314.
   PubMed Web of Science ®Google Scholar
• Peterson SW, Knox NC, Golding GR, et al. A study of the infant nasal microbiome development over the first year of life and in relation to their primary adult caregivers using cpn60 universal target (UT) as a phylogenetic marker. PLoS One. 2016;11(3):3.
   Web of Science ®Google Scholar
• Vandenbroucke JP, Von Elm E, Altman DG, et al. Strengthening the reporting of observational studies in epidemiology (STROBE): explanation and elaboration. PLoS Med. 2007;4(10):e297.
   PubMed Web of Science ®Google Scholar
• National Heart, Lung and Blood Institute. National institute of health, quality assessment tool for observational cohort and cross-sectional studies. Natl Heart Lung and Blood Inst: Bethesda; 2014.
   Google Scholar
• Kim AS, Willis AL, Laubitz D, et al., editors. The effect of maxillary sinus antrostomy size on the sinus microbiome. Wiley Online Library: Int Forum Allergy Rhinol; 2019.
   Google Scholar
• Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, et al. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment. Oncotarget. 2016;7(32):51320.
   PubMedGoogle Scholar
• Xu Y, Teng F, Huang S, et al. Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy. Arch Oral Biol. 2014;59(2):176–186.
   PubMed Web of Science ®Google Scholar
• Galloway-Peña JR, Smith DP, Sahasrabhojane P, et al. Characterisation of oral and gut microbiome temporal variability in hospitalised cancer patients. Genome Med. 2017;9(1):21.
   PubMed Web of Science ®Google Scholar
• Cleland EJ, Bassiouni A, Vreugde S, et al. The bacterial microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes, and patient outcomes. Am J Rhinol Allergy. 2016;30(1):37–43.
   PubMed Web of Science ®Google Scholar
• Hauser LJ, Ir D, Kingdom TT, et al., editors. Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics. Wiley Online Library: Int Forum Allergy Rhinol; 2016.
   Google Scholar
• Meuric V, Le Gall-David S, Boyer E, et al. Signature of microbial dysbiosis in periodontitis. Appl Environ Microbiol. 2017;83(14):14.
   Web of Science ®Google Scholar
• Zhou W, Sailani MR, Contrepois K, et al. Longitudinal multi-omics of host–microbe dynamics in prediabetes. Nature. 2019;569(7758):663–671.
   PubMed Web of Science ®Google Scholar
• Bizzarro S, Laine M, Buijs M, et al. Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis. Sci Rep. 2016;6(1):20205.
   PubMed Web of Science ®Google Scholar
• Mukherjee C, Beall CJ, Griffen AL, et al. High-resolution ISR amplicon sequencing reveals personalised oral microbiome. Microbiome. 2018;6(1):1–15.
   PubMed Web of Science ®Google Scholar
• Shi B, Chang M, Martin J, et al. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. MBio. 2015;6(1):e01926–01914.
   PubMed Web of Science ®Google Scholar
• Liu G, Luan Q, Chen F, et al. Shift in the subgingival microbiome following scaling and root planing in generalised aggressive periodontitis. J Clin Periodontol. 2018;45(4):440–452.
   PubMed Web of Science ®Google Scholar
• Flores GE, Caporaso JG, Henley JB, et al. Temporal variability is a personalised feature of the human microbiome. Genome Biol. 2014;15(12):531.
   PubMed Web of Science ®Google Scholar
• Yang F, Huang S, He T, et al. Microbial basis of oral malodor development in humans. J Dent Res. 2013;92(12):1106–1112.
   PubMed Web of Science ®Google Scholar
• Takeshita T, Tomioka M, Shimazaki Y, et al. Microfloral characterisation of the tongue coating and associated risk for pneumonia‐related health problems in institutionalised older adults. J Am Geriatr Soc. 2010;58(6):1050–1057.
   PubMed Web of Science ®Google Scholar
• Abeles SR, Robles-Sikisaka R, Ly M, et al. Human oral viruses are personal, persistent and gender-consistent. Isme J. 2014;8(9):1753–1767.
   PubMed Web of Science ®Google Scholar
• Goltsman DSA, Sun CL, Proctor DM, et al. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Res. 2018;28(10):1467–1480.
   PubMed Web of Science ®Google Scholar
• Stanaway IB, Wallace JC, Shojaie A, et al. Human oral buccal microbiomes are associated with farmworker status and azinphos-methyl agricultural pesticide exposure. Appl Environ Microbiol. 2017;83(2):e02149–02116.
   PubMed Web of Science ®Google Scholar
• Bouquet J, Tabor DE, Silver JS, et al. Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort. Respirat Res. 2020;21(1):1–13.
   PubMed Web of Science ®Google Scholar
• Wang Z, Singh R, Miller BE, et al. Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study. Thorax. 2018;73(4):331–338.
   PubMed Web of Science ®Google Scholar
• Huang YJ, Sethi S, Murphy T, et al. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014;52(8):2813–2823.
   PubMed Web of Science ®Google Scholar
• Whelan FJ, Heirali AA, Rossi L, et al. Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis. PloS One. 2017;12(3):3.
   Web of Science ®Google Scholar
• Sinha R, Weissenburger-Moser LA, Clarke JL, et al. Short term dynamics of the sputum microbiome among COPD patients. PloS One. 2018;13(3):3.
   Web of Science ®Google Scholar
• Cox MJ, Allgaier M, Taylor B, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PloS One. 2010;5(6):6.
   Web of Science ®Google Scholar
• Sibley CD, Parkins MD, Rabin HR, et al. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad of Sci. 2008;105(39):15070–15075.
   PubMed Web of Science ®Google Scholar
• Bafadhel M, McKenna S, Terry S, et al. Acute exacerbations of chronic obstructive pulmonary disease: identification of biologic clusters and their biomarkers. Am J Respir Crit Care Med. 2011;184(6):662–671.
   PubMed Web of Science ®Google Scholar
• Borewicz K, Pragman AA, Kim HB, et al. Longitudinal analysis of the lung microbiome in lung transplantation. FEMS Microbiol Lett. 2013;339(1):57–65.
   PubMed Web of Science ®Google Scholar
• Hu Y, Zhang Y, Ren X, et al. A case report demonstrating the utility of next generation sequencing in analysing serial samples from the lung following an infection with influenza A (H7N9) virus. J of Clin Virol. 2016;76:45–50.
   Google Scholar
• Kelly BJ, Imai I, Bittinger K, et al. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome. 2016;4(1):7.
   PubMed Web of Science ®Google Scholar
• Sommerstein R, Merz TM, Berger S, et al. Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia. Antimicrob Resist Infect Control. 2019;8(1):81.
   PubMed Web of Science ®Google Scholar
• Liu H-Y, Zhang S-Y, Yang W-Y, et al. Oropharyngeal and sputum microbiomes are similar following exacerbation of chronic obstructive pulmonary disease. Front Microbiol. 2017;8:1163.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Paramasivan S, Bassiouni A, Shiffer A, et al. The international sinonasal microbiome study: a multicentre, multinational characterisation of sinonasal bacterial ecology. Allergy. 2020;75(8):2037–2049.
   PubMed Web of Science ®Google Scholar
• Wu BG, Sulaiman I, Wang J, et al. Severe obstructive sleep apnea is associated with alterations in the nasal microbiome and an increase in inflammation. Am J Respir Crit Care Med. 2019;199(1):99–109.
   PubMed Web of Science ®Google Scholar
• Fricke W, Maddox C, Song Y, et al. Human microbiota characterisation in the course of renal transplantation. Am J Transplant. 2014;14(2):416–427.
   PubMed Web of Science ®Google Scholar
• Mougeot J-LC, Stevens CB, Almon KG, et al. Caries-associated oral microbiome in head and neck cancer radiation patients: a longitudinal study. J Oral Microbiol. 2019;11(1):1586421.
   PubMed Web of Science ®Google Scholar