Publications
- 
      
        
          
        
      
      
Fletcher JR et al. 2025. Cross-feeding interactions between Fusobacterium nucleatumand the glycan forager Segatella oris. bioRxiv. 2025.06.18.660387
Fletcher JR et al. 2025. Commensal-derived short-chain fatty acid disrupt lipid membrane homeostasis in Staphylococcus aureus. mBio. In Press.
Huang Y, Hunter RC. Community Ecology: The framework for next steps in microbiome research in chronic airway disease. European Respiratory Journal. In Press.
Arif SJ, Hoffman KM, et al. 2025. Host-and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression. PLoS pathogens. 21(10):e1013568
Moore, P.J., et al. 2025. Dual oxic-anoxic co-culture enables direct study of anaerobe–host interactions at the airway epithelial interface. mBio, 16(5):e01338-24
Lembke HK et al. 2025. Evaluating the Link between Efflux Pump Expression and Motility Phenotypes in Pseudomonas aeruginosa Treated with Virulence Inhibitors. ACS Infectious Diseases. 11:2080-2089
Roach SN, et al. 2025. Virus-induced perturbations in the mouse microbiome are impacted by microbial experience. mSphere. 10(3):e00563-24.
 - 
      
        
      
      
Fihn CA et al. 2024. Evaluation of expanded 2-aminobenzothiazole library as inhibitors of a model histidine kinase and virulence suppressors in Pseudomonas aeruginosa. Bioorganic Chemistry. 153:107840.
Martin C et al. 2024. Microbiome and metabolome patterns after lung transplantation reflect underlying disease and chronic lung allograft dysfunction. Microbiome. 12(1):196.
Cho RJ et al. 2024. To Compare the Effects of a Standard Versus Hydrophilic Polymer Coated Airway Stent in a Porcine Model: A Randomized, Single-Blinded Study. Journal of Bronchology & Interventional Pulmonology. 31(2):132-8.
 - 
      
        
      
      
Vangay P et al. 2023. Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut. Gut microbes. 15(2):2266627.
Martinson JN et al. 2023. Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities. The ISME Journal. 17(12):2270-8.
Villarreal AR et al. 2023. High-throughput quantification of microbial-derived organic acids in mucin-rich samples via reverse phase high performance liquid chromatography. Journal of Medical Microbiology. 72(6):001708.
Nandula SR et al. 2023. Plasma‐induced inactivation of Staphylococcus aureus biofilms: The role of atomic oxygen and comparison with disinfectants and antibiotics. Plasma Processes and Polymers. 20(1):2200147.
 - 
      
        
      
      
Bonis BM, Hunter RC. JMM Profile: Achromobacter xylosoxidans: the cloak-and-dagger opportunist. Journal of Medical Microbiology. 71(5):001505.
Fletcher JR, et al. 2022. Staphylococcus aureus overcomes anaerobe-derived short-chain fatty acid stress via FadX and the CodY regulon. Journal of Bacteriology. 204(5):e00064-22.
Roach SN et al. 2022. Respiratory influenza virus infection causes dynamic tuft cell and innate lymphoid cell changes in the small intestine. Journal of Virology. 96(9):e00352-22.
Agaronyan K et al. 2022. Tissue remodeling by an opportunistic pathogen triggers allergic inflammation. Immunity. 55(5):895-911.
Yekinni IO. 2022. Design and proof-of-concept evaluation of a touchless connector system for preventing peritoneal dialysis-associated peritonitis. BMJ Innovations. 8(2).
 - 
      
        
      
      
Fay EJ et al. 2021. Natural rodent model of viral transmission reveals biological features of virus population dynamics. Journal of Experimental Medicine. 219(2):e20211220.
Villarreal AR et al. 2021. Draft genome sequence of Scheffersomyces spartinae ARV011, a marine yeast isolate. Microbiology Resource Announcements. 10(45):e00652-21.
O’Toole GA et al. 2021. Model systems to study the chronic, polymicrobial infections in cystic fibrosis: current approaches and exploring future directions. mBio. 12(5):10-128.
Lucas SK et al. 2021. Anaerobic microbiota derived from the upper airways impact Staphylococcus aureus physiology. Infection and immunity. 89(9).
Fiege JK et al. 2021. Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium. PLoS Pathogens. 17(1):e1009292.
Hunter RC. 2021. Host–Microbe Interactions: Wallowing in Mucus Mire. Current Biology. 31(2):R85-8.
 - 
      
        
      
      
Hirsch EB et al. 2020. Ceftolozane-tazobactam and ceftazidime-avibactam activity against β-lactam-resistant Pseudomonas aeruginosa and extended-spectrum β-lactamase-producing Enterobacterales clinical isolates from US medical centres. Journal of global antimicrobial resistance. 22:689-94.
Cho DY et al. 2020. Contribution of short chain fatty acids to the growth of Pseudomonas aeruginosa in rhinosinusitis. Frontiers in cellular and infection microbiology. 10:412.
Valentini TD, Lucas SK, Binder KA et al. 2020. Bioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota. Nature Communications. 11(1):2287.
Flynn JM et al. 2020. Disruption of cross-feeding inhibits pathogen growth in the sputa of patients with cystic fibrosis. mSphere. 5(2):10-128.
Cho DY et al. 2020. The impact of Lactococcus lactis (probiotic nasal rinse) co‐culture on growth of patient‐derived strains of Pseudomonas aeruginosa. International forum of allergy & rhinology Vol. 10, No. 4, pp. 444-449.
Cho DY, Hunter RC, Ramakrishnan VR. The microbiome and chronic rhinosinusitis. Immunology and allergy clinics of North America. 40(2):251.
Glasser NR et al. 2019. Refinement of metabolite detection in cystic fibrosis sputum reveals heme correlates with lung function decline. PLoS One. 14(12):e0226578.
Cameron LC et al. A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans. NPJ Biofilms and Microbiomes. 5(1):20.
McCurtain JL et al. 2019. Agmatine accumulation by Pseudomonas aeruginosa clinical isolates confers antibiotic tolerance and dampens host inflammation. Journal of Medical Microbiology. 68(3):446-55.
Evert C et al. 2019. Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities. ACS Infectious Diseases. 5(3):385-93.
Jagtap PD et al. 2018. BAL fluid metaproteome in acute respiratory failure. American Journal of Respiratory Cell and Molecular Biology. 59(5):648-52.
Adamowicz EM et al. 2018. Cross-feeding modulates antibiotic tolerance in bacterial communities. The ISME Journal. 12(11):2723-35.
Kondeti VS et al. Long-lived and short-lived reactive species produced by a cold atmospheric pressure plasma jet for the inactivation of Pseudomonas aeruginosa and Staphylococcus aureus. Free Radical Biology and Medicine. 124:275-87.
Nelson J et al. 2018. Pulmonary aspiration of sinus secretions in patients with cystic fibrosis. International Forum of Allergy & Rhinology 8(3):385-388.
Lucas SK et al. 2018. 16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients. Journal of Cystic Fibrosis. 17(2):204-12.
Flynn JM et al. 2017. Genome-wide survey of Pseudomonas aeruginosa PA14 reveals a role for the glyoxylate pathway and extracellular proteases in the utilization of mucin. Infection and Immunity. 85(8):10-128.
Breuer RJ et al. 2017. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells. PLoS Genetics. 13(7):e1006878.
Choi HM et al. 2016. Mapping a multiplexed zoo of mRNA expression. Development. 143(19):3632-7.
Gohl DM et al. 2016. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology. 34(9):942-9.
Flynn JM et al. 2016. Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease. PLoS Pathogens. 12(8):e1005846.
Badalamenti JP, Hunter RC. 2015. Complete genome sequence of Achromobacter xylosoxidans MN001, a cystic fibrosis airway isolate. Genome Announcements. 3(4):10-128.
He X et al. 2015. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences. 112(1):244-9.
Whiteson KL et al. 2014. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. American Journal of Respiratory and Critical Care Medicine. 189(11):1309-15.
Hunter RC et al. 2013. Ferrous iron is a significant component of bioavailable iron in cystic fibrosis airways. mBio. 4(4):10-128.
Guélon T et al. Homogenization of Pseudomonas aeruginosa PAO1 biofilms visualized by freeze‐substitution electron microscopy. Biotechnology and Bioengineering. 110(5):1405-18.
Dietrich LEP et al. 2013. Bacterial community morphogenesis is intimately linked to the intracellular redox state. Journal of Bacteriology. 195(7):1371-80.
 - 
      
        
      
      Item description