The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach

References

• Erb-Downward JR, Thompson DL, Han MK, et al. Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One. 2011;6(2):e16384. DOI:10.1371/journal.pone.0016384
   PubMed Web of Science ®Google Scholar
• Einarsson GG, Comer DM, Mcilreavey L, et al. Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers. Thorax. 2016;71(9):795–803. DOI:10.1136/thoraxjnl-2015-207235
   PubMed Web of Science ®Google Scholar
• Morris A, Lung HIV Microbiome Project, Beck JM, Schloss PD, et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013;187(10):1067–1075. DOI:10.1164/rccm.201210-1913OC
   PubMed Web of Science ®Google Scholar
• Dickson RP, Erb-Downward JR, Huffnagle GB. The role of the bacterial microbiome in lung disease. Expert Rev Respir Med. 2013;7(3):245–257.
   PubMed Web of Science ®Google Scholar
• Ramsheh MY, Haldar K, Esteve-Codina A, et al. Lung microbiome composition and bronchial epithelial gene expression in patients with COPD versus healthy individuals: a bacterial 16S rRNA gene sequencing and host transcriptomic analysis. The Lancet Microbe. 2021;2(7):e300–e310. DOI:10.1016/S2666-5247(21)00035-5
   PubMedGoogle Scholar
• Bashiardes S, Zilberman-Schapira G, Elinav E. Use of metatranscriptomics in microbiome research. Bioinform Biol Insights. 2016;10:19–25. DOI:10.4137/BBI.S34610
   PubMed Web of Science ®Google Scholar
• Westermann AJ, Barquist L, Vogel J. Resolving host-pathogen interactions by dual RNA-seq. PLoS Pathog. 2017;13(2):e1006033 DOI:10.1371/journal.ppat.1006033
   PubMed Web of Science ®Google Scholar
• Ren L, Zhang R, Rao J, et al. Transcriptionally active lung microbiome and its association with bacterial biomass and host inflammatory status. mSystems. 2018;3(5):e00199–18., Oct 30DOI:10.1128/mSystems.00199-18
   PubMed Web of Science ®Google Scholar
• Lapperre TS, Snoeck-Stroband JB, Gosman MM. Effect of fluticasone with and without salmeterol on pulmonary outcomes in chronic obstructive pulmonary disease: a randomized trial. Ann Intern Med. 2009;151(8):517–527. DOI:10.7326/0003-4819-151-8-200910200-00004
   PubMed Web of Science ®Google Scholar
• Jeffery P, Endobronchial Biopsy Workshop, Holgate S, Wenzel S. Methods for the assessment of endobronchial biopsies in clinical research: Application to studies of pathogenesis and the effects of treatment. Am J Respir Crit Care Med. 2003;168(6 Pt 2):S1–S17. DOI:10.1164/rccm.200202-150WS
   PubMed Web of Science ®Google Scholar
• Lapperre TS, Postma DS, Gosman MME, et al. Relation between duration of smoking cessation and bronchial inflammation in COPD. Thorax. 2006;61(2):115–121. DOI:10.1136/thx.2005.040519
   PubMed Web of Science ®Google Scholar
• Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–652. doi:10.1038/nbt.1883.Trinity
   PubMed Web of Science ®Google Scholar
• Chen L, Reeve J, Zhang L, et al. GMPR: a robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ. 2018;6:e4600 DOI:10.7717/peerj.4600
   PubMed Web of Science ®Google Scholar
• Oksanen AJ, Blanchet FG, Kindt R, et al. Vegan: community ecology package. R package, version. R Proj Stat Comput Vienna, Austri. 2015;2.2–1.
   Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550550. DOI:10.1186/s13059-014-0550-8
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Drai D, Elmer G, et al. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001;125(1-2):279–284. DOI:10.1016/S0166-4328(01)00297-2
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140. DOI:10.1093/bioinformatics/btp616
   PubMed Web of Science ®Google Scholar
• Reimand J, Kull M, Peterson H, et al. Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007;35:193–200. DOI:10.1093/nar/gkm226
   PubMed Web of Science ®Google Scholar
• Charlson ES, Bittinger K, Haas AR, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184(8):957–963. DOI:10.1164/rccm.201104-0655OC
   PubMed Web of Science ®Google Scholar
• Sze MA, Dimitriu PA, Hayashi S, et al. The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012;185(10):1073–1080. DOI:10.1164/rccm.201111-2075OC
   PubMed Web of Science ®Google Scholar
• Iglesias R, Paramá A, Alvarez MF, et al. Philasterides dicentrarchi (ciliophora, scuticociliatida) as the causative agent of scuticociliatosis in farmed turbot Scophthalmus maximus in Galicia (NW Spain). Dis Aquat Organ. 2001;46(1):47–55. DOI:10.3354/dao046047
   PubMed Web of Science ®Google Scholar
• Parks MB, Nakov T, Ruck EC, et al. Phylogenomics reveals an extensive history of genome duplication in diatoms (bacillariophyta). Am J Bot. 2018;105(3):330–347. DOI:10.1002/ajb2.1056
   PubMed Web of Science ®Google Scholar
• Ditz B, Christenson S, Rossen J, et al. Sputum microbiome profiling in COPD: beyond singular pathogen detection. Thorax. 2020;75(4):338–344. DOI:10.1136/thoraxjnl-2019-214168
   PubMed Web of Science ®Google Scholar
• Jin J, Gan Y, Liu H, et al. Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation. Lung Cancer. 2019;136:129–135. DOI:10.1016/j.lungcan.2019.08.022
   PubMed Web of Science ®Google Scholar
• Goleva E, Jackson LP, Harris JK, et al. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med. 2013;188(10):1193–1201. DOI:10.1164/rccm.201304-0775OC
   PubMed Web of Science ®Google Scholar
• Meecham A, Marshall JF. The ITGB6 gene: its role in experimental and clinical biology. Gene X. 2020;5:100023. DOI:10.1016/j.gene.2019.100023
   PubMedGoogle Scholar
• Kaore NM, Khan Z, Aher AR, et al. Community acquired Roseomonas infection in a pre-existing Tubercular lung lesion. Lung India. 2014;31(3):289–292. DOI:10.4103/0970-2113.135785
   PubMedGoogle Scholar
• Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol. 2011;9(4):244–253.
   PubMed Web of Science ®Google Scholar
• Ogorodova LM, Fedosenko SV, Popenko AS, et al. Comparison study of oropharyngeal microbiota in case of bronchial asthma and chronic obstructive pulmonary disease in different severity levels. Ann Rams. 2015;70(6):669–678. DOI:10.15690/vramn532
   Google Scholar
• Grootjans J, Kaser A, Kaufman RJ, et al. The unfolded protein response in immunity and inflammation. Nat Rev Immunol. 2016;16(8):469–484.
   PubMed Web of Science ®Google Scholar
• Marciniak SJ. Endoplasmic reticulum stress : a key player in human disease. FEBS J. 2019;286(2):228–231. DOI:10.1111/febs.14740
   PubMed Web of Science ®Google Scholar
• Dickens JA, Malzer E, Chambers JE, et al. Pulmonary endoplasmic reticulum stress-scars, smoke, and suffocation. FEBS J. 2019;286(2):322–341. DOI:10.1111/febs.14381
   PubMed Web of Science ®Google Scholar
• Conickx G, Avila Cobos F, Van Den Berge M, et al. MicroRNA profiling in lung tissue and bronchoalveolar lavage of cigarette smoke-exposed mice and in COPD patients: a translational approach. Sci Rep. 2017;7(1):1–14. DOI:10.1038/s41598-017-13265-8
   PubMedGoogle Scholar
• Smet EG, DeEeckhoutte HP, VanCobos FA, et al. The role of miR-155 in cigarette smoke-induced pulmonary in fl ammation and COPD. Mucosal Immunol. 2020;13(3):423–436. DOI:10.1038/s41385-019-0241-6
   PubMed Web of Science ®Google Scholar
• de Goffau MC, Lager S, Salter SJ, et al. Recognizing the reagent microbiome. Nat Microbiol. 2018;3(8):851–853. DOI:10.1038/s41564-018-0202-y
   PubMed Web of Science ®Google Scholar
• Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87. DOI:10.1186/s12915-014-0087-z
   PubMed Web of Science ®Google Scholar
• Eisenhofer R, Minich JJ, Marotz C, et al. Contamination in low microbial biomass microbiome studies: Issues and recommendations. Trends Microbiol. 2019;27(2):105–117. DOI:10.1016/j.tim.2018.11.003
   PubMed Web of Science ®Google Scholar
• Man WH, De Steenhuijsen Piters WAA, Bogaert D. The microbiota of the respiratory tract: Gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259–270. DOI:10.1038/nrmicro.2017.14
   PubMed Web of Science ®Google Scholar
• Wongsurawat T, Jenjaroenpun P, Taylor MK, et al. Rapid sequencing of multiple RNA viruses in their native form. Front Microbiol. 2019;10:260. DOI:10.3389/fmicb.2019.00260
   PubMed Web of Science ®Google Scholar
• Depledge DP, Mohr I, Wilson AC. Going the distance : Optimizing RNA-Seq strategies for transcriptomic analysis of complex viral genomes. J Virol. 2019;93(1):18. pii: e01342. DOI:10.1128/JVI.01342-18
   Web of Science ®Google Scholar