메뉴 건너뛰기




Volumn 3, Issue 5, 2018, Pages

Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status

Author keywords

Airborne microorganisms; Bacterial biomass; Lung microbiome; Lung microbiota; Metatranscriptome; Microbial communities

Indexed keywords


EID: 85071413001     PISSN: None     EISSN: 23795077     Source Type: Journal    
DOI: 10.1128/MSYSTEMS.00199-18     Document Type: Article
Times cited : (64)

References (59)
  • 1
    • 85015657548 scopus 로고    scopus 로고
    • The microbiota of the respiratory tract: gatekeeper to respiratory health
    • Man WH, de Steenhuijsen Piters WA, Bogaert D. 2017. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol 15:259–270. https://doi.org/10.1038/nrmicro.2017.14.
    • (2017) Nat Rev Microbiol , vol.15 , pp. 259-270
    • Man, WH1    de Steenhuijsen Piters, WA2    Bogaert, D.3
  • 2
    • 84942239416 scopus 로고    scopus 로고
    • Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography
    • Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Beck JM, Huffnagle GB, Curtis JL. 2015. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann Am Thorac Soc 12:821–830. https://doi.org/10.1513/AnnalsATS.201501-029OC.
    • (2015) Ann Am Thorac Soc , vol.12 , pp. 821-830
    • Dickson, RP1    Erb-Downward, JR2    Freeman, CM3    McCloskey, L4    Beck, JM5    Huffnagle, GB6    Curtis, JL.7
  • 3
    • 84908045907 scopus 로고    scopus 로고
    • Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease
    • Park H, Shin JW, Park SG, Kim W. 2014. Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease. PLoS One 9:e109710. https://doi.org/10.1371/journal.pone.0109710.
    • (2014) PLoS One , vol.9 , pp. e109710
    • Park, H1    Shin, JW2    Park, SG3    Kim, W.4
  • 4
    • 84943456033 scopus 로고    scopus 로고
    • The airway microbiome in patients with severe asthma: associations with disease features and severity
    • Huang YJ, Nariya S, Harris JM, Lynch SV, Choy DF, Arron JR, Boushey H. 2015. The airway microbiome in patients with severe asthma: associations with disease features and severity. J Allergy Clin Immunol 136: 874–884. https://doi.org/10.1016/j.jaci.2015.05.044.
    • (2015) J Allergy Clin Immunol , vol.136 , pp. 874-884
    • Huang, YJ1    Nariya, S2    Harris, JM3    Lynch, SV4    Choy, DF5    Arron, JR6    Boushey, H.7
  • 6
    • 84872535919 scopus 로고    scopus 로고
    • Xenobiotics shape the physiology and gene expression of the active human gut microbiome
    • Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152:39–50. https://doi.org/10.1016/j.cell.2012.10.052.
    • (2013) Cell , vol.152 , pp. 39-50
    • Maurice, CF1    Haiser, HJ2    Turnbaugh, PJ.3
  • 8
    • 84960510562 scopus 로고    scopus 로고
    • Metagenomic sequencing of the chronic obstructive pulmonary disease upper bronchial tract microbiome reveals functional changes associated with disease severity
    • Cameron SJ, Lewis KE, Huws SA, Lin W, Hegarty MJ, Lewis PD, Mur LA, Pachebat JA. 2016. Metagenomic sequencing of the chronic obstructive pulmonary disease upper bronchial tract microbiome reveals functional changes associated with disease severity. PLoS One 11:e0149095. https://doi.org/10.1371/journal.pone.0149095.
    • (2016) PLoS One , vol.11 , pp. e0149095
    • Cameron, SJ1    Lewis, KE2    Huws, SA3    Lin, W4    Hegarty, MJ5    Lewis, PD6    Mur, LA7    Pachebat, JA.8
  • 12
    • 84979238801 scopus 로고    scopus 로고
    • Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males
    • Lee SW, Kuan CS, Wu LS, Weng JT. 2016. Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males. PLoS One 11:e0159066. https://doi.org/10.1371/journal.pone.0159066.
    • (2016) PLoS One , vol.11 , pp. e0159066
    • Lee, SW1    Kuan, CS2    Wu, LS3    Weng, JT.4
  • 13
    • 85012955503 scopus 로고    scopus 로고
    • Resolving host-pathogen interactions by dual RNA-seq
    • Westermann AJ, Barquist L, Vogel J. 2017. Resolving host-pathogen interactions by dual RNA-seq. PLoS Pathog 13:e1006033. https://doi.org/10.1371/journal.ppat.1006033.
    • (2017) PLoS Pathog , vol.13 , pp. e1006033
    • Westermann, AJ1    Barquist, L2    Vogel, J.3
  • 14
    • 54149090275 scopus 로고    scopus 로고
    • World Health Organization (WHO). WHO Press, Geneva, Switzerland
    • World Health Organization (WHO). 2008. The global burden of disease: 2004 update. WHO Press, Geneva, Switzerland.
    • (2008) The global burden of disease: 2004 update
  • 16
    • 84978863722 scopus 로고    scopus 로고
    • Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions
    • Huang YJ, Erb-Downward JR, Dickson RP, Curtis JL, Huffnagle GB, Han MK. 2017. Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions. Transl Res 179:71–83. https://doi.org/10.1016/j.trsl.2016.06.007.
    • (2017) Transl Res , vol.179 , pp. 71-83
    • Huang, YJ1    Erb-Downward, JR2    Dickson, RP3    Curtis, JL4    Huffnagle, GB5    Han, MK.6
  • 20
    • 84867427320 scopus 로고    scopus 로고
    • The lung microbiome in moderate and severe chronic obstructive pulmonary disease
    • Pragman AA, Kim HB, Reilly CS, Wendt C, Isaacson RE. 2012. The lung microbiome in moderate and severe chronic obstructive pulmonary disease. PLoS One 7:e47305. https://doi.org/10.1371/journal.pone.0047305.
    • (2012) PLoS One , vol.7 , pp. e47305
    • Pragman, AA1    Kim, HB2    Reilly, CS3    Wendt, C4    Isaacson, RE.5
  • 21
    • 84905217349 scopus 로고    scopus 로고
    • Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease
    • Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. 2014. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol 52:2813–2823. https://doi.org/10.1128/JCM.00035-14.
    • (2014) J Clin Microbiol , vol.52 , pp. 2813-2823
    • Huang, YJ1    Sethi, S2    Murphy, T3    Nariya, S4    Boushey, HA5    Lynch, SV.6
  • 22
    • 84966397894 scopus 로고    scopus 로고
    • Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers
    • Einarsson GG, Comer DM, McIlreavey L, Parkhill J, Ennis M, Tunney MM, Elborn JS. 2016. Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers. Thorax 71:795–803. https://doi.org/10.1136/thoraxjnl-2015 -207235.
    • (2016) Thorax , vol.71 , pp. 795-803
    • Einarsson, GG1    Comer, DM2    McIlreavey, L3    Parkhill, J4    Ennis, M5    Tunney, MM6    Elborn, JS.7
  • 25
    • 56749105441 scopus 로고    scopus 로고
    • The many faces of Pseudomonas aeruginosa in chronic obstructive pulmonary disease
    • Murphy TF. 2008. The many faces of Pseudomonas aeruginosa in chronic obstructive pulmonary disease. Clin Infect Dis 47:1534 –1536. https://doi.org/10.1086/593187.
    • (2008) Clin Infect Dis , vol.47 , pp. 1534-1536
    • Murphy, TF.1
  • 26
    • 56749132970 scopus 로고    scopus 로고
    • Chronic Pseudomonas aeruginosa infection in chronic obstructive pulmonary disease
    • Martinez-Solano L, Macia MD, Fajardo A, Oliver A, Martinez JL. 2008. Chronic Pseudomonas aeruginosa infection in chronic obstructive pulmonary disease. Clin Infect Dis 47:1526–1533. https://doi.org/10.1086/ 593186.
    • (2008) Clin Infect Dis , vol.47 , pp. 1526-1533
    • Martinez-Solano, L1    Macia, MD2    Fajardo, A3    Oliver, A4    Martinez, JL.5
  • 28
    • 84876910443 scopus 로고    scopus 로고
    • The integration of T cell migration, differentiation and function
    • Masopust D, Schenkel JM. 2013. The integration of T cell migration, differentiation and function. Nat Rev Immunol 13:309–320. https://doi.org/10.1038/nri3442.
    • (2013) Nat Rev Immunol , vol.13 , pp. 309-320
    • Masopust, D1    Schenkel, JM.2
  • 32
    • 35348941171 scopus 로고    scopus 로고
    • Oral biofilms, periodontitis, and pulmonary infections
    • Paju S, Scannapieco FA. 2007. Oral biofilms, periodontitis, and pulmonary infections. Oral Dis 13:508–512. https://doi.org/10.1111/j.1601-0825.2007.01410a.x.
    • (2007) Oral Dis , vol.13 , pp. 508-512
    • Paju, S1    Scannapieco, FA.2
  • 35
    • 84908074440 scopus 로고    scopus 로고
    • Biogeography and individuality shape function in the human skin metagenome
    • NISC Comparative Sequencing Program
    • Oh J, Byrd AL, Deming C, Conlan S, NISC Comparative Sequencing Program, Kong HH, Segre JA. 2014. Biogeography and individuality shape function in the human skin metagenome. Nature 514:59–64. https://doi.org/10.1038/nature13786.
    • (2014) Nature , vol.514 , pp. 59-64
    • Oh, J1    Byrd, AL2    Deming, C3    Conlan, S4    Kong, HH5    Segre, JA.6
  • 37
    • 58149296036 scopus 로고    scopus 로고
    • Interleukin-17 in host defence against bacterial, mycobacterial and fungal pathogens
    • Curtis MM, Way SS. 2009. Interleukin-17 in host defence against bacterial, mycobacterial and fungal pathogens. Immunology 126:177–185. https://doi.org/10.1111/j.1365-2567.2008.03017.x.
    • (2009) Immunology , vol.126 , pp. 177-185
    • Curtis, MM1    Way, SS.2
  • 39
    • 80053900916 scopus 로고    scopus 로고
    • Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants
    • Mourani PM, Harris JK, Sontag MK, Robertson CE, Abman SH. 2011. Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants. PLoS One 6:e25959. https://doi.org/10.1371/journal.pone.0025959.
    • (2011) PLoS One , vol.6 , pp. e25959
    • Mourani, PM1    Harris, JK2    Sontag, MK3    Robertson, CE4    Abman, SH.5
  • 40
    • 0036310831 scopus 로고    scopus 로고
    • Infection by Ralstonia species in cystic fibrosis patients: identification of R. pickettii and R. mannitolilytica by polymerase chain reaction
    • Coenye T, Vandamme P, LiPuma JJ. 2002. Infection by Ralstonia species in cystic fibrosis patients: identification of R. pickettii and R. mannitolilytica by polymerase chain reaction. Emerg Infect Dis 8:692–696. https://doi.org/10.3201/eid0807.010472.
    • (2002) Emerg Infect Dis , vol.8 , pp. 692-696
    • Coenye, T1    Vandamme, P2    LiPuma, JJ.3
  • 42
    • 0032547330 scopus 로고    scopus 로고
    • Whooping cough caused by Bordetella pertussis and Bordetella parapertussis in an immunized population
    • He Q, Viljanen MK, Arvilommi H, Aittanen B, Mertsola J. 1998. Whooping cough caused by Bordetella pertussis and Bordetella parapertussis in an immunized population. JAMA 280:635–637. https://doi.org/10.1001/jama.280.7.635.
    • (1998) JAMA , vol.280 , pp. 635-637
    • He, Q1    Viljanen, MK2    Arvilommi, H3    Aittanen, B4    Mertsola, J.5
  • 43
    • 84961292871 scopus 로고    scopus 로고
    • High seroprevalence of Bordetella pertussis in patients with chronic obstructive pulmonary disease: a case-control study
    • Hashemi SH, Nadi E, Hajilooi M, Seif-Rabiei MA, Samaei A. 2015. High seroprevalence of Bordetella pertussis in patients with chronic obstructive pulmonary disease: a case-control study. Tanaffos 14:172–176.
    • (2015) Tanaffos , vol.14 , pp. 172-176
    • Hashemi, SH1    Nadi, E2    Hajilooi, M3    Seif-Rabiei, MA4    Samaei, A.5
  • 44
    • 0242286554 scopus 로고    scopus 로고
    • Pertussis toxin plays an early role in respiratory tract colonization by Bordetella pertussis
    • Carbonetti NH, Artamonova GV, Mays RM, Worthington ZE. 2003. Pertussis toxin plays an early role in respiratory tract colonization by Bordetella pertussis. Infect Immun 71:6358–6366. https://doi.org/10.1128/IAI.71.11.6358-6366.2003.
    • (2003) Infect Immun , vol.71 , pp. 6358-6366
    • Carbonetti, NH1    Artamonova, GV2    Mays, RM3    Worthington, ZE.4
  • 45
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, AM1    Lohse, M2    Usadel, B.3
  • 46
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B1    Salzberg, SL.2
  • 47
    • 84870814915 scopus 로고    scopus 로고
    • SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
    • Kopylova E, Noe L, Touzet H. 2012. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28:3211–3217. https://doi.org/10.1093/bioinformatics/bts611.
    • (2012) Bioinformatics , vol.28 , pp. 3211-3217
    • Kopylova, E1    Noe, L2    Touzet, H.3
  • 48
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng Y, Leung HC, Yiu SM, Chin FY. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420 –1428. https://doi.org/10.1093/bioinformatics/ bts174.
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y1    Leung, HC2    Yiu, SM3    Chin, FY.4
  • 49
    • 84871396799 scopus 로고    scopus 로고
    • Ray Meta: scalable de novo metagenome assembly and profiling
    • Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. 2012. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13:R122. https://doi.org/10.1186/gb-2012-13-12-r122.
    • (2012) Genome Biol , vol.13 , pp. R122
    • Boisvert, S1    Raymond, F2    Godzaridis, E3    Laviolette, F4    Corbeil, J.5
  • 52
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/ S0022-2836(05)80360-2.
    • (1990) J Mol Biol , vol.215 , pp. 403-410
    • Altschul, SF1    Gish, W2    Miller, W3    Myers, EW4    Lipman, DJ.5
  • 53
    • 84978910824 scopus 로고    scopus 로고
    • MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data
    • Huson DH, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R. 2016. MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 12:e1004957. https://doi.org/10.1371/journal.pcbi.1004957.
    • (2016) PLoS Comput Biol , vol.12 , pp. e1004957
    • Huson, DH1    Beier, S2    Flade, I3    Gorska, A4    El-Hadidi, M5    Mitra, S6    Ruscheweyh, HJ7    Tappu, R.8
  • 54
    • 84925021592 scopus 로고    scopus 로고
    • Fast and sensitive protein alignment using DIAMOND
    • Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. https://doi.org/10.1038/nmeth.3176.
    • (2015) Nat Methods , vol.12 , pp. 59-60
    • Buchfink, B1    Xie, C2    Huson, DH.3
  • 55
    • 85016149190 scopus 로고    scopus 로고
    • KEGG: new perspectives on genomes, pathways, diseases and drugs
    • Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. 2017. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361. https://doi.org/10.1093/nar/gkw1092.
    • (2017) Nucleic Acids Res , vol.45 , pp. D353-D361
    • Kanehisa, M1    Furumichi, M2    Tanabe, M3    Sato, Y4    Morishima, K.5
  • 57
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
    • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590–D596. https://doi.org/10.1093/nar/gks1219.
    • (2013) Nucleic Acids Res , vol.41 , pp. D590-D596
    • Quast, C1    Pruesse, E2    Yilmaz, P3    Gerken, J4    Schweer, T5    Yarza, P6    Peplies, J7    Glockner, FO.8
  • 58
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–9445. https://doi.org/10.1073/pnas.1530509100.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, JD1    Tibshirani, R.2
  • 59
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57:289–300. https://www.jstor.org/stable/2346101.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.