The first research paper from the Stubbendieck lab is now published in mSystems! In this paper, we were interested in investigating the microbial ecology of the cystic fibrosis (CF) airway, which is colonized with a complex microbiota consisting of oropharyngeal bacteria and pathogens.
Through a reanalysis of 16S rRNA gene amplicon sequencing studies, we determined that oropharyngeal bacteria and pathogens exhibit different colonization dynamics. The former are highly prevalent, but lowly abundant, whereas pathogens are more likely to reach high abundance and dominate the microbiota when present. We predicted that pathogens were negatively associated with each other and with the oropharyngeal bacteria, suggesting that pathogens may be antagonistic. In collaboration with Dr. Erika Lutter (OSU), six undergraduates generated a collection of 1,597 CF isolates from clinical specimens.
Undergrad researcher Sydney Morabbi then performed over 16,000 (!) assays to test each of these CF isolates for inhibitory activity against eight representative bacterial targets. Her results confirmed the predictions from sequencing data: CF pathogens inhibit each other and oropharyngeal bacteria.
We noticed that isolates of Pseudomonas tended to be the most inhibitory, but we often observed variation in the bioactivity of Pseudomonas isolates, even those cultured from the same donor at the same time point. We wanted to know why. We found the metabolomes of these clinical Pseudomonas isolates varied and those differences correlated with the acquisition of different mutations in secondary metabolite biosynthetic gene clusters, suggesting a potential mechanism for the variable antagonism we observed.
I’m super proud of all of the hard work from Sydney and the rest of the lab! If you’re interested, please visit here to check it out!