Unculturables
The Unculturables Group in the Antimicrobial Discovery Center at Northeastern University is focused on growing previously unculturable microorganisms, and identifying the molecular mechanisms responsible for uncultivability. Our work is based on the observation that the vast majority of microorganisms isolated from the environment do not grow in the lab, and are only known by there molecular signatures. This has dramatically limited the fraction of the microbial world that is available for study, and our goal is to gain access to the genetic and biochemical diversity that has been hidden by uncultivability.
Our group uses a number of techniques to grow and understand hard-to-culture microorganisms:
The Chamber. Designed by members of the Lewis and Epstein labs, we utilize in situ growth chambers to allow growth in the natural environment, while isolating the organisms of interest from contamination.
The Trap. A variant of the chamber created by Katya Gavrish of the ADC, this device uses membranes with specific pore sizes to allow penetration of the trap by specific filamentous organisms, such as actinomycetes or fungi. This results in simultaneous selection and growth of the target organisms.
Co-culture. With the hypothesis that some previously unculturable organisms are lacking growth factors normally provided by other bacteria in their environment, we identify organisms that can only grow in proximity to other isolates. In contrast to culture efforts that address growth conditions for single organisms, our approach identifies those growth factors which are missing under laboratory conditions, allowing the culture of significant numbers of organisms from the environment.
Members:
Eric StewartKatya Gavrish
Anthony D'Onofrio
Pallavi Murugkar
Kathrin Witt
Unculturables group publications:
D’Onofrio A., Crawford J.M., Stewart E.J., Witt K., Gavrish E., Epstein S.S., Clardy J., Lewis K. (2008) Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria. Submitted
Gavrish, E., Bollmann, A., Epstein, S.S., Lewis, K. (2008). A trap for in situ cultivation of filamentous actinobacteria. J Microbiol Methods 72(3): 257-62
http://dx.doi.org/10.1016/j.mimet.2007.12.009
Nichols, D., Lewis, K., Orjala, J., Mo, S., Ortenberg, R., O'Connor, P., Zhao, C., Vouros, P., Kaeberlein, T., Epstein, S.S. (2008). Short peptide induces an "uncultivable" microorganism to grow in vitro. Applied and Environmental Microbiology 74(15): 4889-4897
http://aem.asm.org/cgi/reprint/AEM.00393-08v1
Bollmann, A., Lewis, K., Epstein, S.S. (2007). Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73(20): 6386-90
http://aem.asm.org/cgi/reprint/73/20/6386
Kaeberlein, T., Lewis, K., Epstein, S.S. (2002). Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296(5570): 1127-9
http://www.sciencemag.org/cgi/reprint/296/5570/1127.pdf