Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period.
Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients' clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages.IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient's clinical status.
['de Dios Caballero|Juan|J|', 'Vida|Rafael|R|', 'Cobo|Marta|M|', 'Máiz|Luis|L|', 'Suárez|Lucrecia|L|', 'Galeano|Javier|J|', 'Baquero|Fernando|F|', 'Cantón|Rafael|R|', 'Del Campo|Rosa|R|0000-0003-1147-7923']
D000328:Adult D000900:Anti-Bacterial Agents D001419:Bacteria D001501:Bdellovibrio D003198:Computer Simulation D003550:Cystic Fibrosis D004269:DNA, Bacterial D005260:Female D005500:Follow-Up Studies D059014:High-Throughput Nucleotide Sequencing D006801:Humans D008168:Lung D008297:Male D064307:Microbiota D008875:Middle Aged D012336:RNA, Ribosomal, 16S D013183:Sputum D013997:Time Factors D055815:Young Adult
cystic fibrosis lung microbiota predator bacteria next-generation sequencing Bdellovibrio Vampirovibrio antibiotic consumption