Decade-long bacterial community dynamics in cystic fibrosis airways

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549

A new method for non-parametric multivariate analysis of variance

Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

Nadkarni, M. A., Martin, F. E., Jacques, N. A., & Hunter, N. (2002) · Microbiology · doi:10.1099/00221287-148-1-257 · Cited by 1,931

Detection of Anaerobic Bacteria in High Numbers in Sputum from Patients with Cystic Fibrosis

Tunney, M. M., Field, T. R., Moriarty, T. F., Patrick, S., Doering, G., Muhlebach, M. S., Wolfgang, M. C., Boucher, R. C., Gilpin, D. F., McDowell, A., et al. (2008) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.200708-1151oc · Cited by 466

Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients

Cox, M. J., Allgaier, M., Taylor, B., Baek, M. S., Huang, Y. J., Daly, R. A., Karaöz, U., Andersen, G. L., Brown, R., Fujimura, K. E., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011044 · Cited by 458

Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis

Harris, J. K., Groote, M. A. D., Sagel, S. D., Zemanick, E. T., Kapsner, R. K., Penvari, C., Kaess, H., Deterding, R. R., Accurso, F. J., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709804104 · Cited by 373

Characterization of Bacterial Community Diversity in Cystic Fibrosis Lung Infections by Use of 16S Ribosomal DNA Terminal Restriction Fragment Length Polymorphism Profiling

Rogers, G. B., Carroll, M. P., Serisier, D. J., Hockey, P., Jones, G., & Bruce, K. D. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.11.5176-5183.2004 · Cited by 316

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

Sibley, C. D., Parkins, M. D., Rabin, H. R., Duan, K., Nørgaard, J. C., & Surette, M. G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804326105 · Cited by 311

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

Gast, C., Walker, A. W., Stressmann, F. A., Rogers, G. B., Scott, P., Daniels, T. W. V., Carroll, M. P., Parkhill, J., & Bruce, K. D. (2010) · The ISME Journal · doi:10.1038/ismej.2010.175 · Cited by 265

Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa

Klepac‐Ceraj, V., Lemon, K. P., Martin, T. R., Allgaier, M., Kembel, S. W., Knapp, A. A., Lory, S., Brodie, E., Lynch, S. V., Bohannan, B. J. M., et al. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02173.x · Cited by 219

The early-life microbiome: the key to respiratory health?

de Koff, E. M., Pattaroni, C., Marsland, B. J., & Bogaert, D. (2019) · European Respiratory Society eBooks · doi:10.1183/2312508x.10015818 · Cited by 2

Indoor plants regulate the respiratory bacteria of high-altitude migrants and improve their environmental adaptability

Deng, Y. S., Duan, M., Lu, Y., Li, Y., & Liu, L. (2024) · Building and Environment · doi:10.1016/j.buildenv.2024.111368 · Cited by 1

Exploring the human microbiome: Its role and impact on overall health and disease prevention

Alotaibi, F. M., Almazam, ‏. A., Alenezi, S. Z., Alanazi, ‏. H., Lamfon, ‏. A., Albalawi, A. E. A., Al-Nasser, N. S., & Altheyab, S. A. (2018) · International Journal of Health Sciences · doi:10.53730/ijhs.v2ns1.15085 · Cited by 1

The Impact of CFTR Modulators on the Airway Microbiome and the Need for Antibacterial Therapy in Children with Cystic Fibrosis

Vasenyova, Y. O., Вениаминовна, В. И., Сергеевна, В. Е., & Zornikov, D. L. (2025) · Ural Medical Journal · doi:10.52420/umj.24.4.128 · Cited by 1

Assessing the reliability of upper airway sampling for microbiological surveillance in cystic fibrosis

Einarsson, G. G., Lee, A. J., Barry, P. J., Nauman, H., Maher, R. E., McNamara, P. S., Smith, J. A., Jones, A. M., Tunney, M. M., & Lord, R. W. (2025) · Journal of Cystic Fibrosis · doi:10.1016/j.jcf.2025.12.020 · Cited by 1

Paediatrics in Barcelona

Midulla, F., Lombardi, E., Rottier, B. L., Lindblad, A., Grigg, J., Bohlin, K., Rusconi, F., Pohunek, P., & Eber, E. (2014) · European Respiratory Journal · doi:10.1183/09031936.00046414 · Cited by 1

Cystic Fibrosis Cloud database: Un sistema informático para el almacenamiento y manejo de datos clínicos y microbiológicos del paciente con fibrosis quística

Prieto, C. I., Palau, M. J., Martina, P., Achiary, C., Achiary, A., Bettiol, M., Montanaro, P., Cazzola, M. L., Leguizamón, M., Massillo, C., et al. (2016) · Revista Argentina de Microbiología · doi:10.1016/j.ram.2015.11.002 · Cited by 1

Microbiome Therapeutics in Respiratory Illnesses

Shariff, M., & Aditi (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819265-8.00002-4 · Cited by 1

The upper airway microbiome in Hispanic children with cystic fibrosis

Palla, J. B., Thapa, S., Venkatachalam, A., Runge, J. K., Laguna, T. A., & Luna, R. A. (2023) · Pediatric Pulmonology · doi:10.1002/ppul.26484 · Cited by 1

Integrated analysis of microbiome and host transcriptome unveils correlations between lung microbiota and host immunity in bronchoalveolar lavage fluid of pneumocystis pneumonia patients

Zhang, L., Cai, M., Zhang, X., Wang, S., Pang, L., Chen, X., Zheng, C., Sun, Y., Liang, Y., Guo, S., et al. (2024) · Microbes and Infection · doi:10.1016/j.micinf.2024.105374 · Cited by 1

Burkholderia cenocepacia -mediated inhibition of Staphylococcus aureus growth and biofilm formation

Brandt, T. J., Skaggs, H., Hundley, T. C., & Yoder-Himes, D. R. (2025) · Journal of Bacteriology · doi:10.1128/jb.00116-23 · Cited by 1

Differences in Non-Pathogenic Lung-Colonizing Bacteria Among Patients with Different Types of Pneumonia: A Retrospective Study

Hu, C., Yao, S.-F., Li, Y., Wang, Q.-Z., Li, Y., Sun, C., Liu, J., & Zhao, Z. (2025) · Microorganisms · doi:10.3390/microorganisms13092099 · Cited by 1

The lung microbiome in chronic suppurative lung disease: cystic fibrosis and non-cystic fibrosis bronchiectasis

Rogers, G. B., & Huang, Y. J. (2019) · European Respiratory Society eBooks · doi:10.1183/2312508x.10016218 · Cited by 1

Symposium Summaries

(2018) · Pediatric Pulmonology · doi:10.1002/ppul.24151 · Cited by 1

Colistin-resistant microorganisms and cystic fibrosis: microbiological surveillance in an Italian Children’s Hospital

Montemari, A. L., Assanti, V. T. G., Linardos, G., Bonaventura, G. D., Ricciotti, G., & Fiscarelli, E. V. (2019) · Microbiologia medica · doi:10.4081/mm.2019.8163 · Cited by 1

Cystic Fibrosis

Uluer, A., & Marty, F. M. (2015) · Elsevier eBooks · doi:10.1016/b978-1-4557-4801-3.00073-4 · Cited by 2

Future Prospects and Challenges in Targeting Cellular and Molecular Mechanisms in Respiratory Diseases

Verma, N., Thapa, K., & Dua, K. (2021) · Springer eBooks · doi:10.1007/978-981-33-6827-9_39 · Cited by 1

Symposium Summaries

(2019) · Pediatric Pulmonology · doi:10.1002/ppul.22494 · Cited by 1

The infective pulmonary exacerbation in cystic fibrosis : an ecological perspective

Jones, A. (2013) · Spiral (Imperial College London) · doi:10.25560/19230 · Cited by 1

What to Expect When You’re Expectorating: Cystic Fibrosis Exacerbations and Microbiota

Hoffman, L. R., & Surette, M. G. (2013) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201304-086ed · Cited by 1

Alterations of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis. Cystic Fibrosis Transmembrane Conductance Regulator and Antibiotic Effects

Zemanick, E. T., & Wainwright, C. E. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201511-2200ed · Cited by 1

Changes in the Cystic Fibrosis Airway Microbiome after Lung Transplant: The More Things Change, the More They Stay the Same

Aaron, S. D. (2016) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201609-700ed · Cited by 1

Proteogenomics ofPseudomonas aeruginosain Cystic Fibrosis Infections

Yang, L., & Chua, S. L. (2017) · Wiley eBooks · doi:10.1002/9781118960226.ch17 · Cited by 1

The Pitfalls of Polypharmacy and Precision Medicine in Cystic Fibrosis

VanDevanter, D. R., & LiPuma, J. J. (2019) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201902-158ed · Cited by 1

Outdoor Atmospheric Microbial Diversity is Associated with Urban Landscape Structure and Differs from Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial AnalysisPreprint

Stewart, J. D., Kremer, P., Shakya, K. M., Conway, M., & Saad, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.17.157651 · Cited by 1

Comparative Systems Analysis of Opportunistic Gram-Negative Pathogens

Bartell, J. A. (2015) · doi:10.18130/v3726f · Cited by 1

Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients

European Cystic Fibrosis Society Lung Microbiome Working Group (2014) · Springer eBooks · doi:10.1007/978-1-4614-6418-1_470-2 · Cited by 1

Editorial: Respiratory microbiome in health and disease

Zhuang, Y., Ding, T., Zhao, J., & Chai, J. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1335337 · Cited by 1

Phenotypic and Genotypic Characterization of the Streptococci Isolated from Sputum of Adult Cystic Fibrosis Patients

Thornton, C. S. (2013) · Libraries and Cultural Resources (University of Calgary) · doi:10.11575/prism/27331

Pseudomonas aeruginosa and Mucosal Defenses in the Lung

Cohen, T. S. (2012) · Springer eBooks · doi:10.1007/978-1-4614-5326-0_11

Genomic Applications in the Clinical Management of Infectious Diseases

Lefterova, M. I., Banaei, N., & Pinsky, B. A. (2014) · Springer eBooks · doi:10.1007/978-1-4939-0727-4_33

Le microbiome respiratoire : quelles implications pour la pratique ?

Chiron, R. (2013) · Revue des Maladies Respiratoires Actualités · doi:10.1016/s1877-1203(13)70486-5

PULMONARY, SLEEP, AND CRITICAL CARE UPDATE Update in Cystic Fibrosis 2014

Ong, T., & Ramsey, B. W. (2015)

Short-chain Fatty Acids Modulate Bacterial Growth and Airway Epithelial Cell Inflammatory Responses

Ghorbani, P. (2012) · TSpace (University of Toronto)

Mucoviscidose

Regard, L., Lothe-Cartier, M. N., & Burgel, P. (2014) · Revue des Maladies Respiratoires Actualités · doi:10.1016/s1877-1203(14)70005-9

Anti-Infective Therapies in Cystic Fibrosis

Flume, P. A., & VanDevanter, D. R. (2017) · Milestones in drug therapy · doi:10.1007/978-3-0348-0977-1_9

Peripheral immune cell abnormalities associated with cystic fibrosis

Mulcahy, E. M. (2017) · UTAS Research Repository · doi:10.25959/23210792

Three Dimensional Cartography of Microbiome and Metabolome Data onto Radiological Images of the Human LungPreprint

Garg, N., Wang, M., Hyde, E. R., da Silva, R. H. A., Melnik, A. V., Protsyuk, I., Bouslimani, A., Lim, Y. W., Wong, R. L., Humphrey, G. C., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3155764

The future: from the bench to the patient

Boeck, K. D. (2013) · doi:10.2217/ebo.12.526

The effect of Stenotrophomonas maltophilia on Gram-negative cystic fibrosis pathogens.

Stewart, J. (2019) · ThinkIR: The University of Louisville's Institutional Repository (University of Louisville)

Investigation of role of anaerobic bacteria in cystic fibrosis patients

Doğan, Ö., Tunçkanat, F., Cinel, G., Şener, B., Özçelik, U., Yalçın, E., Doğru, D., & Ki̇per, N. (2019) · Tuberkuloz ve Toraks · doi:10.5578/tt.68358

The Airway Microbiome and Bronchopulmonary Dysplasia

Lal, C. V., Dolma, K., & Ambalavanan, N. (2019) · Elsevier eBooks · doi:10.1016/b978-0-323-68353-1.00010-5

mSphere of Influence: a Community To Study Communities

Limoli, D. H. (2020) · mSphere · doi:10.1128/msphere.00047-20

The Pulmonary Microbiome in Cystic Fibrosis

Frost, F. J., Nazareth, D. S., & Wat, D. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.91765

Maintenance of Pulmonary Therapies

Paranjape, S. M., & Mogayzel, P. J. (2020) · Respiratory medicine · doi:10.1007/978-3-030-42382-7_10

Unveiling epidemiology and treatment strategies for efficient management of lung infection in cystic fibrosis

Kanwar, K., Akanksha, N. S., & Wamik, A. (2020) · World Journal of Biology Pharmacy and Health Sciences · doi:10.30574/wjbphs.2020.2.3.0039

Burn- and Trauma-Associated Pulmonary Infection

Sun, Y., Tang, H., Wu, T., Yao, Y.-M., Wang, K., & Xia, Z. (2020) · Springer eBooks · doi:10.1007/978-981-15-7056-8_7

The bronchiectasis microbiome

Rogers, G. B. (2018) · European Respiratory Society eBooks · doi:10.1183/2312508x.10015617

Análisis de cambios genéticos y fenotípicos que acompañan el proceso de adaptación de aislados pertenecientes al complejo Burkholderia cepacia durante la infección crónica en pacientes con fibrosis quística

Leguizamón, M. (2020) · doi:10.35537/10915/112541

Metabolic Modeling of Cystic Fibrosis Airway Microbiota from Patient Samples

Vyas, A. (2021) · ScholarWorks@UMassAmherst (University of Massachusetts Amherst) · doi:10.7275/24145939.0

Dynamics of Respiratory Microbiome Profiles Contributes to Imbalance and Lung Dysbiosis in the Respiratory Tract

Kolla, H. B., Reddy, P. N., & Bramhachari, P. V. (2021) · Springer eBooks · doi:10.1007/978-981-16-3156-6_7

Lung Diseases: Chronic Respiratory Infections

Blasi, F. (2018) · MDPI eBooks · doi:10.3390/books978-3-03897-339-3

Genomic Applications in the Clinical Management of Infectious Diseases

Lefterova, M. I., Suarez, C. J., Banaei, N., & Pinsky, B. A. (2018) · Springer eBooks · doi:10.1007/978-3-319-96830-8_37

Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients

European Cystic Fibrosis Society Lung Microbiome Working Group (2015) · Springer eBooks · doi:10.1007/978-1-4899-7475-4_470

Microbiosis in lung allotransplantation and xenotransplantation: State of the art and future perspective

Guohui, J., Wu, K., Dong, T., Zhang, J., Liu, D., Dong, W., & Chen, J. (2022) · Health care science · doi:10.1002/hcs2.15

The Microbiome in Critically Ill Patients

Tulli, G., & Zuanetti, G. (2022) · Springer eBooks · doi:10.1007/978-3-031-14612-1_7

High-Resolution Methods to Study Microbial Interactions in Biofilms

Domínguez, K., Gannon, A. D., Miller, C. D., & Darch, S. E. (2022) · Springer series on biofilms · doi:10.1007/978-3-031-15349-5_8

Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection

Wagner, B. D., Zemanick, E. T., Sagel, S. D., Robertson, C. E., Stevens, M. J., Mayer-Hamblett, N., Retsch‐Bogart, G. Z., Ramsey, B. W., & Harris, J. K. (2023) · BMC Microbiology · doi:10.1186/s12866-023-03073-8

The Knowns and Unknowns of Chemically Induced Lower Respiratory Tract Microbiota Dysbiosis and Lung Disease

Utembe, W., & Kamng’ona, A. W. (2023) · doi:10.3390/ecas2023-1634

Dealing with Difficult Bugs Before Lung Transplantation

Mehta, N., Lyon, G. M., & Pouch, S. M. (2024) · Organ and tissue transplantation · doi:10.1007/978-3-319-20788-9_16-1

Immune and Microbial Signatures in Immunocompetent and Immunocompromised Patients with PneumoniaPreprint

Zhan, Y., Zhou, J., Li, S., Hu, B., Du, Q., Wang, H., Li, Z., Sun, W., Yang, J., Qiu, Y., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-5225770/v1

Dealing with Difficult Bugs Before Lung Transplantation

Mehta, N., Lyon, G. M., & Pouch, S. M. (2024) · Organ and tissue transplantation · doi:10.1007/978-3-030-36123-5_16

Investigating the Effects of Traffic-Generated Air-Pollution on the Microbiome and Immune Responses in Lungs of Wildtype Mice

Daniel, S. (2020) · doi:10.12794/metadc1752346

Risk factors for antibiotic-resistant respiratory infections among patients requiring ward admission

Ensarıoğlu, K., Özyürek, B. A., Özdemirel, T. Ş., Akkurt, E. S., Özdağ, Ö., İbiş, H., & Şencan, A. S. A. (2025) · Journal of Medicine and Palliative Care · doi:10.47582/jompac.1631919

Microbiomes without boundaries: cystic fibrosis ‘pulmotype’ classifications are dependent on algorithm choice and database size, and indicate continuous variationPreprint

Zhao, C., Lowhorn, R. J., Song, H., Eum, J., & Brown, S. P. (2025) · medRxiv · doi:10.1101/2025.05.07.25326893

Cystic Fibrosis

Hiatt, P., Mann, M. C., & Ruiz, F. E. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-82763-8.00025-x

Vancomycin Sensitization in Pseudomonas aeruginosa is Contingent on Limited Metabolic Flux

Golden, M. M., Siddiqui, S., Ohanaja, V., Post, S. J., & Wuest, W. M. (2025) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c00225

Pseudomonas aeruginosa and Its Unsuspected Ally Lactiplantibacillus plantarum : Enhanced Pathogenicity in A Combined Cystic Fibrosis Sputum – Epithelial Cell Model

Drost, M., & Fuhrmann, G. (2025) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c00759

The role of respiratory viruses in exacerbations of cystic fibrosis in adults

Flight, W. G. (2014) · Research Explorer (The University of Manchester)

Additional file 1 of Longitudinal analysis of sinus microbiota post endoscopic surgery in patients with cystic fibrosis and chronic rhinosinusitis: a pilot study

Wagner Mackenzie, B., Dassi, C., Vivekanandan, A., Zoing, M., Douglas, R. G., & Biswas, K. (2021) · Figshare · doi:10.6084/m9.figshare.14411606

Additional file 4 of Lung function and microbiota diversity in cystic fibrosis

Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H., Ashare, A., Elborn, J. S., Soyza, A. D., Carroll, M. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12062061

Additional file 3 of Lung function and microbiota diversity in cystic fibrosis

Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H., Ashare, A., Elborn, J. S., Soyza, A. D., Carroll, M. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12062058

Additional file 2 of Lung function and microbiota diversity in cystic fibrosis

Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H., Ashare, A., Elborn, J. S., Soyza, A. D., Carroll, M. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12062055

Additional file 5 of Lung function and microbiota diversity in cystic fibrosis

Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H., Ashare, A., Elborn, J. S., Soyza, A. D., Carroll, M. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12062067

Additional file 1 of Lung function and microbiota diversity in cystic fibrosis

Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H., Ashare, A., Elborn, J. S., Soyza, A. D., Carroll, M. P., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12062046

Cystic fibrosis-related diabetes is associated with reduced airway microbial diversity

Diemer, S., Kozjek, K., & Påhlman, L. I. (2026) · Respiratory Research · doi:10.1186/s12931-026-03598-2

Achromobacter & Pandoraea : diversité et évolution adaptative de populations persistantes au cours de la mucoviscidose et dans l'environnement

Dupont, C. (2016) · theses.fr (ABES) · doi:10.70675/6d02bc34z7b72z46c3zbdb7zde2cfad6ddb6

Microbiotes Pulmonaires des patients atteints de mucoviscidose : interactions avec Pseudomonas aeruginosa

Pagès, L. (2016) · theses.fr (ABES) · doi:10.70675/9d450abbzb581z49cez9268z17379d9c31b5

Néogénèse lymphoïde péribronchique induite par l'infection pulmonaire chronique chez la souris : effets d'une immunomodulation par des anticorps monoclonaux ou par des macrolides antibiotiques et non antibiotiques

Regard, L. (2019) · theses.fr (ABES) · doi:10.70675/0fc2d43fz2ce6z48b6za17bz193a5ee24f49

Interactions entre Aspergillus fumigatus et Stenotrophomonas maltophilia au sein d’un biofilm mixte & modulation de leurs réponses aux antimicrobiens

Roisin, L. (2021) · theses.fr (ABES) · doi:10.70675/a0937036z0168z40e6zabe7z3180d5e2e484

Décryptage des interactions bactériennes entre Pseudomonas aeruginosa et Staphylococcus aureus dans un contexte d'infection pulmonaire

Camus, L. (2020) · theses.fr (ABES) · doi:10.70675/ecddb701z1d6fz422fz86d0zc4e6a93d6a98

Drivers and consequences of Staphylococcus aureus adaptation to the lung environment

Ding, X. (2023) · theses.fr (ABES) · doi:10.70675/573abae1zc747z4076z949bza2bdaea8b677

Effet des thérapies protéiques sur l’axe intestin-poumon dans la mucoviscidose

Lussac‐Sorton, F. (2024) · theses.fr (ABES) · doi:10.70675/5167078fzc81dz457az88b6zce4defb6df49

Pseudomonas aeruginosa deploys competitor-specific antagonistic strategiesPreprint

Chen, Z., Wingreen, N. S., & Gitai, Z. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.14.718318

The Updateable Human Virome Database and toolkit: A novel framework for human virome analysisPreprint

Miller, C. J., Pope, C. E., Lavitt, M. L., Caverly, L. J., LiPuma, J. J., Penewit, K. M., Lewis, J. D., Salipante, S. J., & Hoffman, L. R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.01.722327

Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis

Peng, B., & Chang, X. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5264-0_8

A polyvalent phage shapes bacterial dynamics

Crisan, C. V., Tyne, D. V., & Goldberg, J. B. (2026) · Journal of Virology · doi:10.1128/jvi.01363-25

Modulator therapy: rates and stages of respiratory bacteriome restoration in cystic fibrosis patients chronically infected with Pseudomonadota

Voronina, O. L., Ryzhova, N. N., Kunda, M. S., Ermolova, E. I., Amelina, E. L., Kagazezhev, R. U., & Al, G. (2026) · BMC Pulmonary Medicine · doi:10.1186/s12890-026-04356-2

Microbiome analysis of Cystic Fibrosis sputum presents higher sensitivity than the conventional bacterial culture

Volpato, F. C. Z., Lovison, O. V. A., de Lima-Morales, D., Almeida, É. K., Rampelotto, P. H., Martins, A. F., Maróstica, P. J. C., & Barth, A. L. (2026) · The Brazilian Journal of Infectious Diseases · doi:10.1016/j.bjid.2026.105876

Clinical and microbiota alterations in performance horses undergoing long-distance transport

Mahalingam‐Dhingra, A., Bedenice, D., da Silva, D. R. R., Mazan, M. R., Hall, T., Tenney, W. A., & Widmer, G. (2026) · Journal of Veterinary Internal Medicine · doi:10.1093/jvimsj/aalag137

Aspergillus fumigatus coinfection facilitates Pseudomonas aeruginosa chronicity within an ex-vivo pig lung model

Curtis, A., Fitzpatrick, D. A., Harrison, F., & Kavanagh, K. A. (2026) · Microbiology · doi:10.1099/mic.0.001745

Prevotella in the airway: implications for lung health and pathogen defense mediated by Prevotella -host interactions

Stoner, S. N., Fairbanks-Mahnke, A., & Clark, S. E. (2026) · Journal of Bacteriology · doi:10.1128/jb.00228-26

An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research

Whelan, F., & Hall, L. J. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001823

Mitochondria Meet the Lung Microbiome: A Bidirectional Dialogue in Inflammation and Respiratory Diseases

Parolin, C., Gentile, E., Pellegrino, C., Spada, V., Bassi, C., Sabbioni, S., Vitali, B., Pinton, P., & Rimessi, A. (2026) · Biomedicines · doi:10.3390/biomedicines14091965

Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience

Stressmann, F. A., Rogers, G. B., Gast, C., Marsh, P., Vermeer, L. S., Carroll, M. P., Hoffman, L. R., Daniels, T. W. V., Patel, N., Forbes, B., et al. (2012) · Thorax · doi:10.1136/thoraxjnl-2011-200932 · Cited by 153

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis

Carmody, L. A., Caverly, L. J., Foster, B. K., Rogers, M. A. M., Kalikin, L. M., Simon, R. H., VanDevanter, D. R., & LiPuma, J. J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194060 · Cited by 90

Analysis of Changes in Diversity and Abundance of the Microbial Community in a Cystic Fibrosis Patient over a Multiyear Period

Stokell, J. R., Gharaibeh, R. Z., Hamp, T. J., Zapata, M. J., Fodor, A. A., & Steck, T. R. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.02555-14 · Cited by 40

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

Acosta, N., Whelan, F., Somayaji, R., Poonja, A., Surette, M. G., Rabin, H. R., & Parkins, M. D. (2017) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201609-668oc · Cited by 46

Change in composition and structure of bacteria in the CF airway over one year

Stressmann, F. A., Rogers, G. B., Daniels, T. W. V., Lilley, A. K., Carroll, M. P., Jones, G., Forbes, B., Patel, N., & Bruce, K. D. (2009) · Journal of Cystic Fibrosis · doi:10.1016/s1569-1993(09)60131-4