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The vast majority of microorganisms on this planet are "uncultured" - only 1% will grow on a Petri dish. Why do most microorganisms refuse to grow on perfectly nutritious media in the lab? This is a profound paradox that we are trying to solve.
In collaboration with Slava Epstein from our Biology Department, we developed several methods to grow uncultured microorganisms. The basic idea is to grow the organisms in their natural environment in pure culture. We do this my mixing cells from a sample such as marine sediment with agar and placing them in a diffusion chamber, which then goes back into their environment. Pores in the membranes allow compounds from the environment to diffuse in, supporting growth, and bacteria form colonies. But what are the growth factors they receive from their familiar environment?
We noticed that uncultured bacteria growing in the chamber will grow in a Petri dish in the presence of a cultivable organism from the same environment. Using this as a bioassay, we found that the growth factors are siderophores, iron chelators. Surprisingly, a considerable number of uncultured bacteria lost an ability to make their own siderophores and now depend on the kindness of their neighbors. There are undoubtedly many more growth factors and uncultured bacteria to be discovered.
Which brings us to the Human Microbiome - the 1013 bacteria that we host. Most of the species in the human microbiome and uncultured as well, and we are developing a high-throughput method to grow them based on co-culture. The microbiome bacteria also depend on growth factors from their neighbors, and we are in the process of isolating them.
The human microbiome harbors symbionts, but also unwanted organisms that have been linked to diabetes, metabolic syndrome, obesity, IBS and cancer. In collaboration with our drug discovery group, we are developing compounds for specific elimination of particular groups of gut microorganisms, which will allow us to perform Microbiome Manipulation.
Unculturables group publications:
Anthony D'Onofrio, Jason M. Crawford, Eric J. Stewart, Kathrin Witt, Ekaterina Gavrish, Slava Epstein, Jon Clardy, Kim Lewis (2010) Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria. Chemistry & Biology 17(3)256-264. [PDF]
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 [Link]
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 [Link]
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 [Link]
Kaeberlein, T., Lewis, K., Epstein, S.S. (2002). Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296(5570): 1127-9 [PDF]