Bioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota

• Published in: Nature communications Vol. 11; no. 1; p. 2287
• Main Authors: Valentini, Talia D., Lucas, Sarah K., Binder, Kelsey A., Cameron, Lydia C., Motl, Jason A., Dunitz, Jordan M., Hunter, Ryan C.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.05.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 13/31; 14/34; 14/63; 49/23; 631/326/2565/2134; 631/326/2565/855; Amino acids; Amino Acids - metabolism; Antibiotics; Bacteria; Bacteria - classification; Cell culture; Cystic fibrosis; Cystic Fibrosis - microbiology; Ecophysiology; Flow cytometry; Fluorescence; Growth rate; Humanities and Social Sciences; Humans; Lung - microbiology; Lung diseases; Marking; Microbiomes; Microbiota; multidisciplinary; Pathogenesis; Protein Biosynthesis; Pseudomonas aeruginosa - physiology; rRNA; Science; Science (multidisciplinary); Sputum; Sputum - microbiology; Subpopulations; Taxa; Taxonomy; Translation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16163-2

Culture-independent studies of cystic fibrosis lung microbiota have provided few mechanistic insights into the polymicrobial basis of disease. Deciphering the specific contributions of individual taxa to CF pathogenesis requires comprehensive understanding of their ecophysiology at the site of infection. We hypothesize that only a subset of CF microbiota are translationally active and that these activities vary between subjects. Here, we apply bioorthogonal non-canonical amino acid tagging (BONCAT) to visualize and quantify bacterial translational activity in expectorated sputum. We report that the percentage of BONCAT-labeled (i.e. active) bacterial cells varies substantially between subjects (6-56%). We use fluorescence-activated cell sorting (FACS) and genomic sequencing to assign taxonomy to BONCAT-labeled cells. While many abundant taxa are indeed active, most bacterial species detected by conventional molecular profiling show a mixed population of both BONCAT-labeled and unlabeled cells, suggesting heterogeneous growth rates in sputum. Differentiating translationally active subpopulations adds to our evolving understanding of CF lung disease and may help guide antibiotic therapies targeting bacteria most likely to be susceptible. Bioorthogonal non-canonical amino acid tagging (BONCAT) coupled with flow cytometry (FACS) has been utilized to profile active microbiome of environmental samples. Here, the authors combine BONCAT-FACS and 16 S rRNA sequencing to characterize the translational activity of bacterial communities within sputum derived from stable cystic fibrosis patients.