P60: Culturing airway polymicrobial communities under continuous flow conditions

Microbes play a very important role in maintaining the balance in natural ecosystems and are present as members of diverse, complex communities in these environments. In humans these communities are present on multiple body sites and the upper respiratory tract harbors a complex microbiome. Some in vitro microfluidic and in vivo models are available to study the airway microbial communities, however these methods are expensive, limited and it is not very feasible to do experiments manipulating the community. A robust culture-based approach that can depict true patterns of microbial growth in natural environments has been developed in this study to investigate spatial-temporal changes in bacterial populations, and the community structure-function relationship in vitro. Matrix-embedded synthetic bacterial communities (comprised of aerobes, facultative anaerobes and obligate anaerobes) were grown in continuous flow cell systems. Additionally, the structure of communities propagated in these systems was compared to those in static and shaken batch cultures. Our data shows that reproducible stable bacterial communities can be propagated with both methods wherein the community composition varies considerably with the approach used. However, only matrix-embedded communities cultured under continuous flow conditions could successfully retain obligate anaerobes when flow cell systems were operated in an aerobic environment. The rapid establishment of natural oxygen, pH and nutrient gradients in these flow cells helps maintain the original composition of the community, and this optimized method will be used for culturing diverse and complex natural communities from clinical samples like nasal swabs and sputum in near future experiments.