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cystic fibrosis

  • Open Access
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways
    Minireview | Host-Microbe Biology
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways

    Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical...

    Rutvij A. Khanolkar, Shawn T. Clark, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman
  • Open Access
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy
    Research Article | Clinical Science and Epidemiology
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy

    Subjects with cystic fibrosis battle polymicrobial lung infections throughout their lifetime. Although antibiotic therapy is a principal treatment for CF lung disease, we have little understanding of how antibiotics affect the CF lung microbiome and metabolome and how much the community changes on daily timescales. By analyzing 594 longitudinal CF sputum samples from six adult subjects, we show that the sputum microbiome and metabolome...

    Ruma Raghuvanshi, Karla Vasco, Yoshiki Vázquez-Baeza, Lingjing Jiang, James T. Morton, Danxun Li, Antonio Gonzalez, Lindsay DeRight Goldasich, Gregory Humphrey, Gail Ackermann, Austin D. Swafford, Douglas Conrad, Rob Knight, Pieter C. Dorrestein, Robert A. Quinn
  • Open Access
    Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses
    Research Article | Ecological and Evolutionary Science
    Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses

    Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship.

    Sara M. Clifton, Ted Kim, Jayadevi H. Chandrashekhar, George A. O’Toole, Zoi Rapti, Rachel J. Whitaker
  • Open Access
    Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
    Research Article | Host-Microbe Biology
    Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis

    Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same...

    Alexey V. Melnik, Yoshiki Vázquez-Baeza, Alexander A. Aksenov, Embriette Hyde, Andrew C. McAvoy, Mingxun Wang, Ricardo R. da Silva, Ivan Protsyuk, Jason V. Wu, Amina Bouslimani, Yan Wei Lim, Tal Luzzatto-Knaan, William Comstock, Robert A. Quinn, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S. Brouha, Nuno Bandeira, Grace Y. Lin, Forest Rohwer, Douglas J. Conrad, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein, Neha Garg
  • Open Access
    Temperate Bacteriophages from Chronic <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility
    Research Article | Host-Microbe Biology
    Temperate Bacteriophages from Chronic Pseudomonas aeruginosa Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility

    Pseudomonas aeruginosa is a key opportunistic respiratory pathogen in patients with cystic fibrosis and non-cystic fibrosis bronchiectasis. The genomes of these pathogens are enriched with mobile genetic elements including diverse temperate phages. While the temperate phages of the Liverpool epidemic strain have been shown to be active in the human lung and enhance...

    Mohammad A. Tariq, Francesca L. C. Everest, Lauren A. Cowley, Rosanna Wright, Giles S. Holt, Hazel Ingram, Liberty A. M. Duignan, Andrew Nelson, Clare V. Lanyon, Audrey Perry, John D. Perry, Stephen Bourke, Michael A. Brockhurst, Simon H. Bridge, Anthony De Soyza, Darren L. Smith
  • Open Access
    Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
    Research Article | Novel Systems Biology Techniques
    Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

    Cystic fibrosis (CF) is a genetic disease in which chronic airway infections and lung inflammation result in respiratory failure. CF airway infections are usually caused by bacterial communities that are difficult to eradicate with available antibiotics. Using species abundance data for clinically stable adult CF patients assimilated from three published studies, we developed a metabolic model of CF airway communities to better...

    Michael A. Henson, Giulia Orazi, Poonam Phalak, George A. O’Toole
  • Open Access
    Metapopulation Structure of CRISPR-Cas Immunity in <em>Pseudomonas aeruginosa</em> and Its Viruses
    Research Article | Ecological and Evolutionary Science
    Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses

    Pseudomonas aeruginosa is a widespread opportunistic pathogen and a major cause of morbidity and mortality in cystic fibrosis patients. Microbe-virus interactions play a critical role in shaping microbial populations, as viral infections can kill microbial populations or contribute to gene flow among microbes. Investigating how...

    Whitney E. England, Ted Kim, Rachel J. Whitaker
  • Open Access
    Balance Trees Reveal Microbial Niche Differentiation
    Research Article | Ecological and Evolutionary Science
    Balance Trees Reveal Microbial Niche Differentiation

    By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss .

    James T. Morton, Jon Sanders, Robert A. Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A. Navas-Molina, Se Jin Song, Jessica L. Metcalf, Embriette R. Hyde, Manuel Lladser, Pieter C. Dorrestein, Rob Knight
  • Open Access
    Long-Term Evolution of <span class="named-content genus-species" id="named-content-1">Burkholderia multivorans</span> during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection

    Bacteria may become genetically and phenotypically diverse during long-term colonization of cystic fibrosis (CF) patient lungs, yet our understanding of within-host evolutionary processes during these infections is lacking. Here we combined current genome sequencing technologies and detailed phenotypic profiling of the opportunistic pathogen Burkholderia multivorans...

    Inês N. Silva, Pedro M. Santos, Mário R. Santos, James E. A. Zlosnik, David P. Speert, Sean W. Buskirk, Eric L. Bruger, Christopher M. Waters, Vaughn S. Cooper, Leonilde M. Moreira
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