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Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways

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  • 1.

    Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, et al. Prevalence of Streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol. 2012;194:4709–17.

    CAS 
    Article 

    Google Scholar 

  • 2.

    Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, et al. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One. 2012;7:e45001.

    CAS 
    Article 

    Google Scholar 

  • 3.

    Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA. 2012;109:13769–74.

    CAS 
    Article 

    Google Scholar 

  • 4.

    Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S, et al. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J. 2011;5:20–9.

    Article 

    Google Scholar 

  • 5.

    Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, et al. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci USA. 2007;104:20529–33.

    CAS 
    Article 

    Google Scholar 

  • 6.

    Brown PS, Pope CE, Marsh RL, Qin X, McNamara S, Gibson R, et al. Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota. Ann Am Thorac Soc. 2014;11:1049–55.

    Article 

    Google Scholar 

  • 7.

    Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, et al. Regional isolation drives bacterial diversification within cystic fibrosis lungs. Cell Host Microbe. 2015;18:307–19.

    CAS 
    Article 

    Google Scholar 

  • 8.

    Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci USA. 2008;105:15070–5.

    CAS 
    Article 

    Google Scholar 

  • 9.

    van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, et al. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J. 2011;5:780–91.

    Article 

    Google Scholar 

  • 10.

    Zhao J, Carmody LA, Kalikin LM, Li J, Petrosino JF, Schloss PD, et al. Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS One. 2012;7:e33127.

    CAS 
    Article 

    Google Scholar 

  • 11.

    Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, et al. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc. 2013;10:179–87.

    Article 

    Google Scholar 

  • 12.

    Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010;5:e11044.

    Article 

    Google Scholar 

  • 13.

    Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, et al. Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax. 2012;67:867–73.

    Article 

    Google Scholar 

  • 14.

    Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA. 2012;109:5809–14.

    CAS 
    Article 

    Google Scholar 

  • 15.

    Rogers GB, Bruce KD, Hoffman LR. How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med. 2017;23:536–43.

    Article 

    Google Scholar 

  • 16.

    Widder S, Knapp S. Microbial metabolites in cystic fibrosis: a target for future therapy? Am J Respir Cell Mol Biol. 2019;61:132–3.

  • 17.

    Mahboubi MA, Carmody LA, Foster BK, Kalikin LM, VanDevanter DR, LiPuma JJ. Culture-based and culture-independent bacteriologic analysis of cystic fibrosis respiratory specimens. J Clin Microbiol. 2016;54:613–9.

    CAS 
    Article 

    Google Scholar 

  • 18.

    Carmody LA, Caverly LJ, Foster BK, Rogers MAM, Kalikin LM, Simon RH, et al. Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis. PLoS One. 2018;13:e0194060.

    Article 

    Google Scholar 

  • 19.

    Zhao J, Li J, Schloss PD, Kalikin LM, Raymond TA, Petrosino JF, et al. Effect of sample storage conditions on cultureindependent bacterial community measures in cystic fibrosis sputum specimens. J Clin Microbiol 2011;49:3717–8.

  • 20.

    Hnizdo E, Yu L, Freyder L, Attfield M, Lefante J & Glindmeyer HW. The precision of longitudinal lung function measurements: Monitoring and interpretation. Occup Environ Med 2005;62:695–701.

  • 21.

    Konstan MW, Wagener JS, VanDevanter DR. Characterizing aggressiveness and predicting future progression of CF lung disease. J Cyst Fibros. 2009;8:S15–19.

    Article 

    Google Scholar 

  • 22.

    Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16s rRNA-based studies. PLoS One. 2011;6:e27310.

    CAS 
    Article 

    Google Scholar 

  • 23.

    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.

    CAS 
    Article 

    Google Scholar 

  • 24.

    Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The ribosomal database project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37:D141–145.

    CAS 
    Article 

    Google Scholar 

  • 25.

    Sung J, Kim S, Cabatbat JJT, Jang S, Jin YS, Jung GY, et al. Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nat Commun 2017;8:15393.

  • 26.

    Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8:e1002687.

    CAS 
    Article 

    Google Scholar 

  • 27.

    Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One. 2012;7:e30126.

    CAS 
    Article 

    Google Scholar 

  • 28.

    Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509:357–60.

    CAS 
    Article 

    Google Scholar 

  • 29.

    Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, et al. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome 2013;1:27.

  • 30.

    Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, et al. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome 2015;3:12.

  • 31.

    de Dios Caballero J, Vida R, Cobo M, Maiz L, Suarez L, Galeano J, et al. Individual patterns of complexity in cystic fibrosis lung microbiota, including predator bacteria, over a 1-year period. mBio 2017;8::e00959–17.

  • 32.

    Whelan, FJ, Heirali AA, Rossi L, Rabin HR, Parkins MD, & Surette MG. Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis. PLoS One 2017:12:e0172811.

  • 33.

    Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, et al. Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation. mSystems 2016;1.

  • 34.

    Douglas, GM, Maffei, VJ, Zaneveld, JR, Yurgel, SN, Brown JR, Taylor CM, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 2020;38:685–8.

  • 35.

    Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, et al. The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res 2018;46:D633–D639.

  • 36.

    Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, et al. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci Adv 2018;4:eaau1908.

  • 37.

    Quinn RA, Whiteson K, Lim YW, Zhao J, Conrad D, LiPuma JJ, et al. Ecological networking of cystic fibrosis lung infections. NPJ Biofilms Microbiomes. 2016;2:4.

    Article 

    Google Scholar 

  • 38.

    Pradeu T, Vivier E. The discontinuity theory of immunity. Sci Immunol. 2016;1:AAG0479.

  • 39.

    Flynn JM, Niccum D, Dunitz JM, Hunter RC. Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease. PLoS Pathog. 2016;12:e1005846.

    Article 

    Google Scholar 

  • 40.

    Adamowicz EM, Flynn J, Hunter RC, Harcombe WR. Cross-feeding modulates antibiotic tolerance in bacterial communities. ISME J. 2018;12:2723–35.

    CAS 
    Article 

    Google Scholar 

  • 41.

    Rose MC & Voynow JA. Respiratory tract mucin genes and mucin glycoproteins in health and disease. Physiol Rev 2006;86:245–78.

  • 42.

    Tailford LE, Crost EH, Kavanaugh D. & Juge N. Mucin glycan foraging in the human gut microbiome. Front Genet 2015;6:81.

  • 43.

    Wheeler KM, Carcamo-Oyarce G, Turner BS, Dellos-Nolan S, Co JY, Lehoux S, et al. Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection. Nat Microbiol 2019;4:2146–54.

  • 44.

    Twomey KB, O’Connell OJ, McCarthy Y, Dow JM, O’Toole GA, Plant BJ, et al. Bacterial cis-2-unsaturated fatty acids found in the cystic fibrosis airway modulate virulence and persistence of Pseudomonas aeruginosa. ISME J 2012;6:939–50.

  • 45.

    Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, et al. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J 2017;50:1700832.

  • 46.

    Lu J, Carmody LA, Opron K, Simon RH, Kalikin LM, Caverly LJ, et al. Parallel analysis of cystic fibrosis sputum and saliva’reveals overlapping communities and an opportunity for sample decontamination. mSystems 2020;5.

  • 47.

    Jones KL, Hegab AH, Hillman BC, Simpson KL, Jinkins PA, Grisham MB, et al. Elevation of nitrotyrosine and nitrate concentrations in cystic fibrosis sputum. Pediatr Pulmonol 2000;30:79–85.

  • 48.

    Quinn RA, Lim YW, Maughan H, Conrad D, Rohwer F, Whiteson KL. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio. 2014;5:e00956–00913.

    Article 

    Google Scholar 

  • 49.

    Mirkovic B, Murray MA, Lavelle GM, Molloy K, Azim AA, Gunaratnam C, et al. The role of short-chain fatty acids, produced by anaerobic bacteria, in the cystic fibrosis airway. Am J Respir Crit Care Med. 2015;192:1314–24.

    CAS 
    Article 

    Google Scholar 

  • 50.

    Trompette A, Gollwitzer ES, Pattaroni C, Lopez-Mejia IC, Riva E, Pernot J, et al. Dietary fiber confers protection against flu by shaping Ly6c(-) patrolling monocyte hematopoiesis and CD8(+) t cell metabolism. Immunity. 2018;48:992–1005.e1008.

    CAS 
    Article 

    Google Scholar 

  • 51.

    Flynn JM, Phan C, Hunter RC. Genome-wide survey of Pseudomonas aeruginosa PA14 reveals a role for the glyoxylate pathway and extracellular proteases in the utilization of mucin. Infect Immun. 2017;85:e00182–17.

  • 52.

    Jorth P, Ehsan Z, Rezayat A, Caldwell E, Pope C, Brewington JJ, et al. Direct lung sampling indicates that established pathogens dominate early infections in children with cystic fibrosis. Cell Rep. 2019;27:1190–204.e1193.

    CAS 
    Article 

    Google Scholar 

  • 53.

    Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol. 2019;37:783–92.

    CAS 
    Article 

    Google Scholar 

  • 54.

    Cowley ES, Kopf SH, LaRiviere A, Ziebis W, Newman DK. Pediatric cystic fibrosis sputum can be chemically dynamic, anoxic, and extremely reduced due to hydrogen sulfide formation. mBio. 2015;6:e00767.

    CAS 
    Article 

    Google Scholar 

  • 55.

    Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, et al. Lung function and microbiota diversity in cystic fibrosis. Microbiome 2020;8:45.


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