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Niche partitioning of a pathogenic microbiome driven by chemical gradients.

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC.

Sci Adv. 2018 Sep 26;4(9):eaau1908. doi: 10.1126/sciadv.aau1908. eCollection 2018 Sep.


Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung.

Quinn RA, Lim YW, Maughan H, Conrad D, Rohwer F, Whiteson KL.

MBio. 2014 Mar 18;5(2):e00956-13. doi: 10.1128/mBio.00956-13.


Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities.

Lim YW, Schmieder R, Haynes M, Willner D, Furlan M, Youle M, Abbott K, Edwards R, Evangelista J, Conrad D, Rohwer F.

J Cyst Fibros. 2013 Mar;12(2):154-64. doi: 10.1016/j.jcf.2012.07.009. Epub 2012 Aug 28.


Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period.

de Dios Caballero J, Vida R, Cobo M, Máiz L, Suárez L, Galeano J, Baquero F, Cantón R, Del Campo R.

MBio. 2017 Sep 26;8(5). pii: e00959-17. doi: 10.1128/mBio.00959-17.


Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC.

Microbiome. 2019 Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3.


The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations.

Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, Wolfgang MC.

PLoS One. 2012;7(9):e45001. doi: 10.1371/journal.pone.0045001. Epub 2012 Sep 26.


A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.

Bacci G, Mengoni A, Fiscarelli E, Segata N, Taccetti G, Dolce D, Paganin P, Morelli P, Tuccio V, De Alessandri A, Lucidi V, Bevivino A.

Int J Mol Sci. 2017 Jul 29;18(8). pii: E1654. doi: 10.3390/ijms18081654.


The metabolic footprint of the airway bacterial community in cystic fibrosis.

Narayanamurthy V, Sweetnam JM, Denner DR, Chen LW, Naureckas ET, Laxman B, White SR.

Microbiome. 2017 Jun 30;5(1):67. doi: 10.1186/s40168-017-0289-z.


Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum.

Hahn A, Sanyal A, Perez GF, Colberg-Poley AM, Campos J, Rose MC, Pérez-Losada M.

J Microbiol Methods. 2016 Nov;130:95-99. doi: 10.1016/j.mimet.2016.09.002. Epub 2016 Sep 5.


The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning 16 Years.

Acosta N, Whelan FJ, Somayaji R, Poonja A, Surette MG, Rabin HR, Parkins MD.

Ann Am Thorac Soc. 2017 Aug;14(8):1288-1297. doi: 10.1513/AnnalsATS.201609-668OC.


Chronic but not intermittent infection with Pseudomonas aeruginosa is associated with global changes of the lung microbiome in cystic fibrosis.

Boutin S, Graeber SY, Stahl M, Dittrich AS, Mall MA, Dalpke AH.

Eur Respir J. 2017 Oct 5;50(4). pii: 1701086. doi: 10.1183/13993003.01086-2017. Print 2017 Oct. No abstract available.


The Microbiome in Cystic Fibrosis.

Huang YJ, LiPuma JJ.

Clin Chest Med. 2016 Mar;37(1):59-67. doi: 10.1016/j.ccm.2015.10.003. Epub 2015 Dec 23. Review.


Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.

Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C.

Microbiome. 2017 Feb 10;5(1):20. doi: 10.1186/s40168-017-0234-1.


[The lung microbiome in 2015: a window on chronic lung diseases].

Andréjak C, Delhaes L.

Med Sci (Paris). 2015 Nov;31(11):971-8. doi: 10.1051/medsci/20153111011. Epub 2015 Nov 17. Review. French.


Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis.

Acosta N, Heirali A, Somayaji R, Surette MG, Workentine ML, Sibley CD, Rabin HR, Parkins MD.

Thorax. 2018 Nov;73(11):1016-1025. doi: 10.1136/thoraxjnl-2018-211510. Epub 2018 Aug 22.


The evolving dynamics of the microbial community in the cystic fibrosis lung.

McGuigan L, Callaghan M.

Environ Microbiol. 2015 Jan;17(1):16-28. doi: 10.1111/1462-2920.12504. Epub 2014 Jun 3. Review.


Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities.

van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J, Bruce KD.

ISME J. 2011 May;5(5):780-91. doi: 10.1038/ismej.2010.175. Epub 2010 Dec 9.


A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients.

Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15070-5. doi: 10.1073/pnas.0804326105. Epub 2008 Sep 23.


Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.


Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.

Hogan DA, Willger SD, Dolben EL, Hampton TH, Stanton BA, Morrison HG, Sogin ML, Czum J, Ashare A.

PLoS One. 2016 Mar 4;11(3):e0149998. doi: 10.1371/journal.pone.0149998. eCollection 2016.

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