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Background  Multiple independent culture-based studies have identified the presence of  Pseudomonas aeruginosa  in respiratory samples as a positive risk factor for bronchiolitis obliterans syndrome (BOS). Yet, culture-independent microbiological techniques have identified a negative association between  Pseudomonas  species and BOS. Our objective was to investigate whether there may be a unifying explanation for these apparently dichotomous results.    Methods  We performed bronchoscopies with bronchoalveolar lavage (BAL) on lung transplant recipients (46 procedures in 33 patients) and 26 non-transplant control subjects. We analyzed bacterial communities in the BAL fluid using qPCR and pyrosequencing of 16S rRNA gene amplicons and compared the culture-independent data with the clinical metadata and culture results from these subjects.    Findings  Route of bronchoscopy (via nose or via mouth) was not associated with changes in BAL microbiota (p = 0.90). Among the subjects with positive  Pseudomonas  bacterial culture,  P. aeruginosa  was also identified by culture-independent methods. In contrast, a distinct  Pseudomonas  species,  P. fluorescens , was often identified in asymptomatic transplant subjects by pyrosequencing but not detected via standard bacterial culture. The subject populations harboring these two distinct pseudomonads differed significantly with respect to associated symptoms, BAL neutrophilia, bacterial DNA burden and microbial diversity. Despite notable differences in culturability, a global database search of UM Hospital Clinical Microbiology Laboratory records indicated that  P. fluorescens  is commonly isolated from respiratory specimens.    Interpretation  We have reported for the first time that two prominent and distinct  Pseudomonas  species ( P. fluorescens  and  P. aeruginosa ) exist within the post-transplant lung microbiome, each with unique genomic and microbiologic features and widely divergent clinical associations, including presence during acute infection.

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Changes in the Lung Microbiome following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations